Proteins having pneumococcal capsule degrading activity and methods of use

ABSTRACT

Provided herein is a protein, referred to as a Pn3Pase protein, that degrades the capsular polysaccharide of serotype 3 Streptococcus pneumoniae. The disclosure includes a genetically modified cell that includes a Pn3Pase protein, and compositions that include the protein, the polynucleotide encoding the protein, the genetically modified cell, or a combination thereof. Also provided are methods for using a Pn3Pase protein, including methods for contacting a S. pneumoniae having a type III capsular polysaccharide with a Pn3Pase protein, increasing deposition of at least one complement component on the surface of a S. pneumoniae, treating an infection in a subject, treating a symptom in a subject, decreasing colonization of a subject by S. pneumoniae, or a combination thereof.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application Ser. No. 62/545,094, filed Aug. 14, 2017, and U.S. Provisional Application Ser. No. 62/652,046, filed Apr. 3, 2018, each of which is incorporated by reference herein.

GOVERNMENT FUNDING

This invention was made with government support under 1R01AI123383-01A1, awarded by the National Institutes of Health. The government has certain rights in the invention.

SEQUENCE LISTING

This application contains a Sequence Listing electronically submitted via EFS-Web to the United States Patent and Trademark Office as an ASCII text file entitled “2018-08-10-SequenceListing-02710201_ST25.txt” having a size of 99 kilobytes and created on Aug. 10, 2018. The information contained in the Sequence Listing is incorporated by reference herein.

BACKGROUND

Diseases caused by Streptococcus pneumoniae (Spn) have long been a major threat to human health with alarming mortality rates. One disease, pneumonia, affects approximately 450 million people globally (7% of the population) and results in about 4 million deaths per year. Prevention of pneumococcal disease relies today on vaccination of the susceptible population. Pneumococcal vaccines are made empirically and are variably/poorly immunogenic especially among young children, the elderly, and immunocompromised individuals. The mainstay of drug therapy for pneumococcal disease is antibiotic treatment; however, widespread use of antibiotics against S. pneumoniae has led to spread of drug resistance pneumococcal strains. In 2015, according to CDC, pneumococcal bacteria were resistant to one or more antibiotics in 30% of the cases.

S. pneumoniae has over 90 unique capsular serotypes, each differing in monosaccharide composition and linkage, as well as other modifications such as acetylation. While conjugate vaccines have been effective for preventing carriage and disease caused by most S. pneumoniae serotypes included in the vaccines, the exception has been serotype 3.

SUMMARY

Described herein is the identification and cloning of a Pn3Pase gene expressed by a Paenibacillus strain. The Pn3Pase enzyme degrades the capsular polysaccharide of the S. pneumoniae serotype 3, which is among the most virulent serotypes with high morbidity and mortality rates. Capsular polysaccharide is the major virulence factor of S. pneumoniae (Spn), and most unencapsulated bacteria are not infective. The enzyme successfully degrades the capsular polysaccharide on the surface of the live bacterium. Moreover, the bacterium is susceptible to phagocytosis in the presence of the enzyme.

Provided herein is a genetically modified cell that includes a mature Pn3Pase protein. In one embodiment, the genetically modified cell includes a polynucleotide including a coding region, where the coding region includes a nucleotide sequence encoding a mature Pn3Pase protein. The protein can include an amino acid sequence having at least 80% identity with an amino acid sequence selected from SEQ ID NO:2, where the amino terminal amino acid is selected from any one of residues 2 to 64 of SEQ ID NO:2 and the carboxy terminal amino acid is residue 1545 of SEQ ID NO:2. In one embodiment, the protein includes an amino acid sequence having at least 80% identity with amino acids 41-1545 of SEQ ID NO:2. In one embodiment, the genetically modified cell can be a eukaryotic cell, such as a mammalian cell, a yeast cell, or an insect cell. In one embodiment, the genetically modified cell can be a prokaryotic cell, such as E. coli. In one embodiment, the protein includes a heterologous amino acid sequence, such as a tag.

Also provided herein are compositions. In one embodiment, a composition includes the genetically modified cell. In one embodiment, a composition includes an isolated, optionally purified, mature P3nPase protein. In one embodiment, a composition includes an isolated polynucleotide, where the polynucleotide includes a coding region encoding a mature Pn3Pase protein. The mature P3nPase protein can include an amino acid sequence having at least 80% identity with an amino acid sequence selected from SEQ ID NO:2, where the amino terminal amino acid is selected from residues 2 to 64 of SEQ ID NO:2 and the carboxy terminal amino acid is residue 1545 of SEQ ID NO:2. In one embodiment, the protein includes an amino acid sequence having at least 80% identity with amino acids 41-1545 of SEQ ID NO:2. In one embodiment, a composition further includes a pharmaceutically acceptable carrier.

Also provided herein are methods. In one embodiment, a method includes incubating a cell under conditions suitable for expression of a protein having Pn3Pase activity. The cell can include a polynucleotide including a coding region, where the coding region includes a nucleotide sequence encoding a mature Pn3Pase protein, where the protein has Pn3Pase activity, and where the cell expresses the mature Pn3Pase protein under suitable conditions. The protein can include an amino acid sequence having at least 80% identity with an amino acid sequence selected from SEQ ID NO:2, where the amino terminal amino acid is selected from any one of residues 2 to 64 of SEQ ID NO:2 and the carboxy terminal amino acid is residue 1545 of SEQ ID NO:2. In one embodiment, the protein includes an amino acid sequence having at least 80% identity with amino acids 41-1545 of SEQ ID NO:2. The cell can be a wild-type cell, e.g., a Paenibacillus strain, such as Paenibacillus sp. 32352, or a genetically modified cell where the polynucleotide encoding the is an exogenous polynucleotide. The method can further include isolating or purifying the protein. In one embodiment, the cell can be a eukaryotic cell, such as a mammalian cell, a yeast cell, or an insect cell. In one embodiment, the genetically modified cell can be a prokaryotic cell, such as E. coli. In one embodiment, the protein includes a heterologous amino acid sequence, such as a tag.

In one embodiment, a method includes contacting a Streptococcus pneumoniae including a type III capsular polysaccharide with a mature Pn3Pase protein, where the contacting is under conditions suitable for enzymatic hydrolysis of type III capsular polysaccharide, where the amount of type III capsular polysaccharide on the surface of the S. pneumoniae is reduced compared to the S. pneumoniae that is not contacted with the Pn3Pase protein. In another embodiment, a method is for increasing deposition of at least one complement component on the surface of a Streptococcus pneumoniae. In one embodiment, the method can include contacting a Streptococcus pneumoniae including a type III capsular polysaccharide with a mature Pn3Pase protein, where the deposition of at least one complement component on the surface of the S. pneumoniae is increased compared to the S. pneumoniae that is not contacted with the Pn3Pase protein. The protein can include an amino acid sequence having at least 80% identity with an amino acid sequence selected from SEQ ID NO:2, where the amino terminal amino acid is selected from any one of residues 2 to 64 of SEQ ID NO:2 and the carboxy terminal amino acid is residue 1545 of SEQ ID NO:2. In one embodiment, The protein includes an amino acid sequence having at least 80% identity with amino acids 41-1545 of SEQ ID NO:2. In one embodiment, the S. pneumoniae is present in conditions suitable for replication of the S. pneumoniae. In one embodiment, the mature Pn3Pase protein is an isolated Pn3Pase protein. In one embodiment, the contacting includes exposing the S. pneumoniae to a genetically modified cell that expresses the mature Pn3Pase protein. In one embodiment, the S. pneumoniae has increased susceptibility to phagocytosis by macrophages, increased complement-mediated killing by neutrophils, or a combination thereof, compared to the S. pneumoniae that is not contacted with the Pn3Pase protein. In one embodiment, the S. pneumoniae is present in a subject.

In one embodiment, a method is for treating an infection in a subject and includes administering an effective amount of a composition that includes a mature Pn3Pase protein having Pn3Pase activity to a subject having or at risk of having an infection caused by a serotype 3 S. pneumoniae. In one embodiment, the method is for treating a symptom in a subject and includes administering an effective amount of a composition including a mature Pn3Pase protein having Pn3Pase activity to a subject having or at risk of having an infection caused by a serotype 3 S. pneumoniae. In one embodiment, a method is for decreasing colonization in a subject and includes administering an effective amount of a composition including a including a mature Pn3Pase protein having P3nPase activity to a subject colonized by or at risk of being colonized by a serotype 3 S. pneumoniae. The protein can include an amino acid sequence having at least 80% identity with an amino acid sequence selected from SEQ ID NO:2, where the amino terminal amino acid is selected from any one of residues 2 to 64 of SEQ ID NO:2 and the carboxy terminal amino acid is residue 1545 of SEQ ID NO:2. In one embodiment, the protein includes an amino acid sequence having at least 80% identity with amino acids 41-1545 of SEQ ID NO:2. In one embodiment, the subject is a human.

Also provided is a mature Pn3Pase protein disclosed herein for use in therapy, mature Pn3Pase protein disclosed herein for use as a medicament, and a mature Pn3Pase protein disclosed herein for use in the treatment of a condition.

Further provided is the use of a mature Pn3Pase protein disclosed herein for preparation of a medicament for the treatment of pneumonia, pneumococcal meningitis, otitis media, bacteremia, sepsis, or a combination thereof; a composition including a mature P3nPase protein described herein for use in treating or preventing an infection or a symptom caused by a serotype 3 S. pneumoniae; and a protein, composition, or method including one or more features described herein.

As used herein, “genetically modified cell” refers to a cell into which has been introduced an exogenous polynucleotide, such as an expression vector. For example, a cell is a genetically modified cell by virtue of introduction into a suitable cell of an exogenous polynucleotide that is foreign to the cell. “Genetically modified cell” also refers to a cell that has been genetically manipulated such that endogenous nucleotides have been altered. For example, a cell is a genetically modified cell by virtue of introduction into a suitable cell of an alteration of endogenous nucleotides. An example of a genetically modified cell is one having an altered regulatory sequence, such as a promoter, to result in increased or decreased expression of an operably linked endogenous coding region.

As used herein, the term “protein” refers broadly to a polymer of two or more amino acids joined together by peptide bonds. The term “protein” also includes molecules which contain more than one protein joined by a disulfide bond, or complexes of proteins that are joined together, covalently or noncovalently, as multimers (e.g., dimers, tetramers). Thus, the terms peptide, oligopeptide, enzyme, and polypeptide are all included within the definition of protein and these terms are used interchangeably. It should be understood that these terms do not connote a specific length of a polymer of amino acids, nor are they intended to imply or distinguish whether the protein is produced using recombinant techniques, chemical or enzymatic synthesis, or is naturally occurring.

As used herein, a “mature protein” refers to a protein having an amino acid sequence that is identical to or having structural similarity with a protein that has been processed after translation to result in its final form. Post-translation processing can include N-terminal processing or C-terminal truncation. As used herein, a “preprocessed protein” refers to a protein that has been translated from a mRNA and has not undergone post-translation processing to result in a mature protein.

As used herein, an “isolated” substance, for instance a protein, is one that has been removed from its natural environment, produced using recombinant techniques, or chemically or enzymatically synthesized. For instance, a protein or a polynucleotide can be isolated. Preferably, a substance is purified, i.e., is at least 60% free, preferably at least 75% free, and most preferably at least 90% free from other components with which they are naturally associated.

As used herein, the term “polynucleotide” refers to a polymeric form of nucleotides of any length, either ribonucleotides or deoxynucleotides, and includes both double- and single-stranded RNA and DNA. A polynucleotide can be obtained directly from a natural source, or can be prepared with the aid of recombinant, enzymatic, or chemical techniques. A polynucleotide can be linear or circular in topology. A polynucleotide may be, for example, a portion of a vector, such as an expression or cloning vector, or a fragment. A polynucleotide may include nucleotide sequences having different functions, including, for instance, coding regions, and non-coding regions such as regulatory regions.

As used herein, a “detectable moiety” or “label” is a molecule that is detectable, either directly or indirectly, by spectroscopic, photochemical, biochemical, immunochemical, or chemical means. For example, useful labels include ³²P, fluorescent dyes, electron-dense reagents, enzymes and their substrates (e.g., as commonly used in enzyme-linked immunoassays, e.g., alkaline phosphatase and horse radish peroxidase), biotin-streptavidin, digoxigenin, proteins such as antibodies, or haptens and proteins for which antisera or monoclonal antibodies are available. The label or detectable moiety is typically bound, either covalently, through a linker or chemical bound, or through ionic, van der Waals or hydrogen bonds to the molecule to be detected.

As used herein, the terms “coding region” and “coding sequence” are used interchangeably and refer to a nucleotide sequence that encodes a protein and, when placed under the control of appropriate regulatory sequences expresses the encoded protein. The boundaries of a coding region are generally determined by a translation start codon at its 5′ end and a translation stop codon at its 3′ end. A “regulatory sequence” is a nucleotide sequence that regulates expression of a coding sequence to which it is operably linked. Non-limiting examples of regulatory sequences include promoters, enhancers, transcription initiation sites, translation start sites, translation stop sites, and transcription terminators. The term “operably linked” refers to a juxtaposition of components such that they are in a relationship permitting them to function in their intended manner. A regulatory sequence is “operably linked” to a coding region when it is joined in such a way that expression of the coding region is achieved under conditions compatible with the regulatory sequence.

A polynucleotide that includes a coding region may include heterologous nucleotides that flank one or both sides of the coding region. As used herein, “heterologous nucleotides” refer to nucleotides that are not normally present flanking a coding region that is present in a wild-type cell. Thus, a polynucleotide that includes a coding region and heterologous nucleotides is not a naturally occurring molecule. For instance, a coding region present in a wild-type microbe and encoding a Pn3Pase protein is flanked by homologous sequences, and any other nucleotide sequence flanking the coding region is considered to be heterologous. Examples of heterologous nucleotides include, but are not limited to regulatory sequences. Typically, heterologous nucleotides are present in a polynucleotide described herein through the use of standard genetic and/or recombinant methodologies well known to one skilled in the art. A polynucleotide described herein may be included in a suitable vector.

A protein described herein may include heterologous amino acids present at the N-terminus, the C-terminus, or a combination thereof. As used herein, “heterologous amino acids” refer to amino acids that are not normally present flanking a protein that is naturally present in a wild-type cell. Thus, a protein that includes heterologous amino acids is not a naturally occurring molecule. For instance, a naturally occurring Pn3Pase protein present in a wild-type microbe does not have additional amino acids at either the N-terminal end or the C-terminal end, and any other amino acids present at the N-terminal end or the C-terminal end are considered to be heterologous. Examples of heterologous amino acid sequences are described herein, and include, but are not limited to affinity purification tags. Typically, heterologous amino acids are present in a protein described herein through the use of standard genetic and/or recombinant methodologies well known to one skilled in the art.

As used herein, an “exogenous polynucleotide” refers to a polynucleotide that is not normally or naturally found in a cell. As used herein, the term “endogenous polynucleotide” refers to a polynucleotide that is normally or naturally found in a cell. An “endogenous polynucleotide” is also referred to as a “native polynucleotide.”

The terms “complement” and “complementary” as used herein, refer to the ability of two single stranded polynucleotides to base pair with each other, where an adenine on one strand of a polynucleotide will base pair to a thymine or uracil on a strand of a second polynucleotide and a cytosine on one strand of a polynucleotide will base pair to a guanine on a strand of a second polynucleotide. Two polynucleotides are complementary to each other when a nucleotide sequence in one polynucleotide can base pair with a nucleotide sequence in a second polynucleotide. For instance, 5′-ATGC and 5′-GCAT are complementary. The term “substantial complement” and cognates thereof as used herein refer to a polynucleotide that is capable of selectively hybridizing to a specified polynucleotide under stringent hybridization conditions. Stringent hybridization can take place under a number of pH, salt, and temperature conditions. The pH can vary from 6 to 9, preferably 6.8 to 8.5. The salt concentration can vary from 0.15 M sodium to 0.9 M sodium, and other cations can be used as long as the ionic strength is equivalent to that specified for sodium. The temperature of the hybridization reaction can vary from 30° C. to 80° C., preferably from 45° C. to 70° C. Additionally, other compounds can be added to a hybridization reaction to promote specific hybridization at lower temperatures, such as at or approaching room temperature. Among the compounds contemplated for lowering the temperature requirements is formamide. Thus, a polynucleotide is typically substantially complementary to a second polynucleotide if hybridization occurs between the polynucleotide and the second polynucleotide. As used herein, “specific hybridization” refers to hybridization between two polynucleotides under stringent hybridization conditions.

In the comparison of two amino acid sequences, structural similarity may be referred to by percent “identity” or may be referred to by percent “similarity.” “Identity” refers to the presence of identical amino acids. “Similarity” refers to the presence of not only identical amino acids but also the presence of conservative substitutions. The sequence similarity between two proteins is determined by aligning the residues of the two proteins (e.g., a candidate amino acid sequence and a reference amino acid sequence, such as a mature Pn3Pase protein, e.g., amino acids 41-1545 of SEQ ID NO:2) to optimize the number of identical amino acids along the lengths of their sequences; gaps in either or both sequences are permitted in making the alignment in order to optimize the number of shared amino acids, although the amino acids in each sequence must nonetheless remain in their proper order. Sequence similarity may be determined, for example, using sequence techniques such as the BESTFIT algorithm in the GCG package (Madison Wis.), or the Blastp program of the BLAST 2 search algorithm, as described by Tatusova, et al. (FEMS Microbiol Lett 1999, 174:247-250), and available through the World Wide Web, for instance at the internet site maintained by the National Center for Biotechnology Information, National Institutes of Health. Preferably, sequence similarity between two amino acid sequences is determined using the Blastp program of the BLAST 2 search algorithm. Preferably, the default values for all BLAST 2 search parameters are used. In the comparison of two amino acid sequences using the BLAST search algorithm, structural similarity is referred to as “identities.” Thus, reference to a protein described herein, such as a mature Pn3Pase protein, e.g., amino acids 41-1545 of SEQ ID NO:2, can include a protein with at least 80% identity, at least 81% identity, at least 82% identity, at least 83% identity, at least 84% identity, at least 85% identity, at least 86% identity, at least 87% identity, at least 88% identity, at least 89% identity, at least 90% identity, at least 91% identity, at least 92% identity, at least 93% identity, at least 94% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity with the reference protein. Alternatively, reference to a protein described herein, such as a mature Pn3Pase protein, e.g., amino acids 41-1545 of SEQ ID NO:2, can include a protein with at least 80% similarity, at least 81% similarity, at least 82% similarity, at least 83% similarity, at least 84% similarity, at least 85% similarity, at least 86% similarity, at least 87% similarity, at least 88% similarity, at least 89% similarity, at least 90% similarity, at least 91% similarity, at least 92% similarity, at least 93% similarity, at least 94% similarity, at least 95% similarity, at least 96% similarity, at least 97% similarity, at least 98% similarity, or at least 99% similarity with the reference protein.

The sequence similarity between two polynucleotides is determined by aligning the residues of the two polynucleotides (e.g., a candidate nucleotide sequence and a reference nucleotide sequence encoding a mature Pn3Pase protein) to optimize the number of identical nucleotides along the lengths of their sequences; gaps in either or both sequences are permitted in making the alignment in order to optimize the number of shared nucleotides, although the nucleotides in each sequence must nonetheless remain in their proper order. Sequence similarity may be determined, for example, using sequence techniques such as GCG FastA (Genetics Computer Group, Madison, Wis.), MacVector 4.5 (Kodak/IBI software package) or other suitable sequencing programs or methods known in the art. Preferably, sequence similarity between two nucleotide sequences is determined using the Blastn program of the BLAST 2 search algorithm, as described by Tatusova, et al. (1999, FEMS Microbiol Lett., 174:247-250), and available through the World Wide Web, for instance at the internet site maintained by the National Center for Biotechnology Information, National Institutes of Health. Preferably, the default values for all BLAST 2 search parameters are used. In the comparison of two nucleotide sequences using the BLAST search algorithm, sequence similarity is referred to as “identities.” The sequence similarity is typically at least 50% identity, at least 55% identity, at least 60% identity, at least 65% identity, at least 70% identity, at least 75% identity, at least 80% identity, at least 81% identity, at least 82% identity, at least 83% identity, at least 84% identity, at least 85% identity, at least 86% identity, at least 87% identity, at least 88% identity, at least 89% identity, at least 90% identity, at least 91% identity, at least 92% identity, at least 93% identity, at least 94% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity.

As used herein, “in vitro” refers to an artificial environment and to processes or reactions that occur within an artificial environment. In vitro environments can include, but are not limited to, a test tube. As used herein, the term “in vivo” refers to a natural environment that is within the body of a subject.

Conditions that “allow” an event to occur or conditions that are “suitable” for an event to occur, such as an enzymatic reaction, or “suitable” conditions are conditions that do not prevent such events from occurring. Thus, these conditions permit, enhance, facilitate, and/or are conducive to the event.

The term “and/or” means one or all of the listed elements or a combination of any two or more of the listed elements.

The words “preferred” and “preferably” refer to embodiments of the disclosure that may afford certain benefits, under certain circumstances. However, other embodiments may also be preferred, under the same or other circumstances. Furthermore, the recitation of one or more preferred embodiments does not imply that other embodiments are not useful, and is not intended to exclude other embodiments from the scope of the disclosure.

The terms “comprises” and variations thereof do not have a limiting meaning where these terms appear in the description and claims.

It is understood that wherever embodiments are described herein with the language “include,” “includes,” or “including,” and the like, otherwise analogous embodiments described in terms of “consisting of” and/or “consisting essentially of” are also provided.

Unless otherwise specified, “a,” “an,” “the,” and “at least one” are used interchangeably and mean one or more than one.

Also herein, the recitations of numerical ranges by endpoints include all numbers subsumed within that range (e.g., 1 to 5 includes 1, 1.5, 2, 2.75, 3, 3.80, 4, 5, etc.).

For any method disclosed herein that includes discrete steps, the steps may be conducted in any feasible order. And, as appropriate, any combination of two or more steps may be conducted simultaneously.

Reference throughout this specification to “one embodiment,” “an embodiment,” “certain embodiments,” or “some embodiments,” etc., means that a particular feature, configuration, composition, or characteristic described in connection with the embodiment is included in at least one embodiment of the disclosure. Thus, the appearances of such phrases in various places throughout this specification are not necessarily referring to the same embodiment of the disclosure. Furthermore, the particular features, configurations, compositions, or characteristics may be combined in any suitable manner in one or more embodiments.

The above summary of the present disclosure is not intended to describe each disclosed embodiment or every implementation of the present disclosure. The description that follows more particularly exemplifies illustrative embodiments. In several places throughout the application, guidance is provided through lists of examples, which examples can be used in various combinations. In each instance, the recited list serves only as a representative group and should not be interpreted as an exclusive list.

In the description herein particular embodiments may be described in isolation for clarity. Unless otherwise expressly specified that the features of a particular embodiment are incompatible with the features of another embodiment, certain embodiments can include a combination of compatible features described herein in connection with one or more embodiments.

BRIEF DESCRIPTION OF THE FIGURES

The following detailed description of illustrative embodiments of the present disclosure may be best understood when read in conjunction with the following drawings.

FIG. 1 shows a repeating unit structure of Streptococcus pneumoniae (Spn) serotype 3 capsular polysaccharide.

FIG. 2 shows an amino acid alignment of seven glycoside hydrolases from Paenibacillus. WP_079915027.1 (SEQ ID NO:2), WP_113018908.1 (SEQ ID NO:4), WP_068663733.1 (SEQ ID NO:5), KRE82476.1 (SEQ ID NO:6), WP_082593776.1 (SEQ ID NO:7), WP_056617367.1 (SEQ ID NO:8), and WP_028553222.1 (SEQ ID NO:9).

FIG. 3 shows culture of Paenibacillus sp. 32352 in minimal medium with Pn3P as carbon source. (FIG. 3A) Growth of Paenibacillus sp. 32352 (Pbac) on minimal medium plus 2% (w/v) glucose, Pn3P, cellulose, or nothing as carbon source. (FIG. 3B) SDS-PAGE coomassie blue stained gel of concentrated culture supernatant of Pbac grown on glucose (lane 1) or Pn3P (lane 2). (FIG. 3C) Proposed locus of Pn3P utilization organization based on the Rapid Annotation Server (Aziz et al. 2008, BMC Genomics 9, 75) (RAST) annotation. (FIG. 3D) Real-Time PCR of select genes within putative locus in Pbac grown on 2% glucose or Pn3P, shown as fold change in expression in Pn3P culture versus glucose culture.

FIG. 4 shows Pn3Pase identification and domain schematic of primary amino acid sequence. (FIG. 4A) Amino acid sequence (SEQ ID NO:2) and accession of Pn3Pase. (FIG. 4B) Separation of recombinant Pn3Pase depolymerized tritium radioisotope labeled Pn3P by size exclusion chromatography, measured by counts per minute in each 1 ml fraction. (FIG. 4C) Dot blot of recombinant Pn3Pase depolymerized cold Pn3P probed with Pn3P monoclonal antibody. (FIG. 4D) Schematic of predicted domains of Pn3Pase by InterPro. (FIG. 4E) A nucleotide sequence (SEQ ID NO:1) encoding a Pn3Pase.

FIG. 5 shows identification of oligosaccharide products by electrospray ionization mass spectrometry. Separation of oligosaccharide products (FIG. 5A) and mass spectra of the tetrasaccharide (FIG. 5B) and the hexasaccharide (FIG. 5C). Experimental molecular weights and the accuracies are shown in Table 1.

FIG. 6 shows Nuclear Magnetic Resonance characterization of oligosaccharide products. 1H NMR spectrum (A), 2D HSQC NMR spectrum (B), and 2D COSY NMR spectrum (C) of the Pn3 tetrasaccharide. 1H NMR spectrum (D), 2D HSQC NMR spectrum (E), and 2D COSY NMR spectrum (F) of the Pn3 hexasaccharide.

FIG. 7 shows activity assessment of Pn3Pase. (FIG. 7A) Time course assay of recombinant Pn3Pase depolymerized tritium radioisotope labeled Pn3P separated by size exclusion chromatography, measured by counts per minute in each 1 ml fraction. (FIG. 7B) Optimization of recombinant Pn3Pase in three different buffer conditions, measured by concentration of glucuronic acid reducing end generated in μg/ml. (C) Metal dependence determination with Mg2+ and Ca2+ reaction supplements, measured by concentration of glucuronic acid reducing end generated in μg/ml. Statistical significance was determined with the two-tailed Student t-test ** P<0.01

FIG. 8 shows Pn3Pase treatment of live, growing type 3 Streptococcus pneumoniae WU2 strain. (FIG. 8A) Growth curve of WU2 in THY broth in the presence of 100 ug/ml Pn3Pase following the OD at 600 nm. (FIG. 8B-8C) Competition ELISA in which acapsular WU2, or Pn3Pase treated WU2 was used to compete for Pn3P specific antibody binding to Pn3P coated ELISA plate. Data is presented as percent inhibition of antibody binding. (FIG. 8D) Transmission Electron Microscopy of WU2 (upper left), acapsular derivative (upper right), and representative Pn3Pase treated WU2 (bottom panels). Statistical significance was determined with the two-tailed Student t test ** P<0.01, *** P<0.001.

FIG. 9 shows the effects of Pn3Pase treatment on type 3 Spn viability. (FIG. 9A) Growth curve of WU2 in THY broth in the presence of 100 μg/ml Pn3Pase following the OD at 600 nm. (FIG. 9B) WU2 survival in PBS in the presence of 100 μg/ml active or heat inactivated Pn3Pase.

FIG. 10 shows depleting the capsule on live type 3 Spn by Pn3Pase treatment. (FIG. 10A-B) Competition ELISA in which acapsular WU2, WU2 treated with heat-inactivated Pn3Pase, or WU2 treated with Pn3Pase at two different concentrations (2 μg/ml or 10 μg/ml) were used to compete for Pn3P specific antibody binding to Pn3P coated ELISA plate. Data is presented as percent inhibition of antibody binding. Statistical significance was determined with the two-tailed Student t test ** P<0.01, *** P<0.001. Transmission electron microscopy images of WU2 mock treated with 2 μg/ml heat-inactivated Pn3Pase (FIG. 10C), acapsular WU2 strain (FIG. 10D) and 2 μg/ml active-Pn3Pase treated WU2 (E). Bottom panels are imaged at 15000× direct magnification and top panels are imaged at 10000× direct magnification (C-E).

FIG. 11 shows macrophage uptake of Pn3Pase treated type 3 Spn. (FIG. 11A) RAW 264.7 macrophage containing fluorescent streptococci following Heat inactivated (left) or active (right) Pn3Pase treatment. Streptococci, CF SE, green. Macrophage, Biotinylated-WGA, Streptavidin-APC, red. (FIG. 11B) Influence of Pn3Pase treatment and complement on macrophage uptake of CF SE labeled Spn quantified by flow cytometry. (FIG. 11C) Pn3Pase dose dependent effect on the percent of fluorescent phagocytes. Statistical significance was determined with the two-tailed Student t test *** P<0.001.

FIG. 12 shows effect of Pn3Pase treatment on complement deposition on Spn surface. Analysis of mouse complement deposition on Pn3Pase treated or untreated type 3 Spn by flow Cytometry. Quantification by Mean fluorescent intensity (MFI) of FITC-A was calculated from gating of Hoechst-positive cells. Statistical significance was determined with the two-tailed Student t test ** P<0.01, *** P<0.001, ns=not significant.

FIG. 13 shows effect of Pn3Pase treatment on complement mediated killing by neutrophils. Complement mediated killing capacity of differentiated HL-60 cells on Pn3Pase treated Spn. Percent survival was calculated as each duplicate reaction normalized to mean values obtained for control samples (reactions without HL60 cells, 100% survival). Statistical significance was determined with the two-tailed Student t test *** P<0.001, ** P<0.01, * P<0.05, ns=not significant.

FIG. 14 shows intranasal colonization with type 3 Spn. Ability of Pn3Pase treatment to reduce Spn colonization in nasopharynx of BALB/c mice. (FIG. 14A) Groups of mice were intranasally inoculated with 106 log-phase bacteria in 10 μl PBS. All inocula were chased with either 50 μg of Pn3Pase or buffer control (10 μl). Groups were dosed with the enzyme at either day 0 (WU2+Pn3Pase*1), day 0 and 3 (WU2+Pn3Pase*2), or day 0, 3, and 7 (WU2+Pn3Pase*3). Bacterial load was quantified on day 10. Serial dilutions of nasal lavage fluid were plated in duplicate to determine CFU values. (FIG. 14B) IL-6 and (FIG. 14C) TNFα concentrations in nasal lavage fluid was determined by ELISA. Statistical significance was determined with the two-tailed Student t test * P<0.05, ** P<0.01.

FIG. 15 shows protective ability of Pn3Pase. Assessment of ability of Pn3Pase to protect BALB/c mice from lethal challenge. Groups of mice were infected through intraperitoneal administration of 5×103 log-phase virulent type 3 Spn. Inactivated group is heat inactivated Pn3Pase. *Shown are the effect of a single dose of 5 μg or 0.5 μg, administered at time 0, 12, or 24 hours post infection, n=5 mice per group.

DETAILED DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS Proteins

Provided herein are genetically modified cells and methods for using the cells. The genetically modified cells can produce a protein having Pn3Pase activity. A protein having Pn3Pase activity is referred to herein as a Pn3Pase protein or a Pn3Pase. A protein having Pn3Pase activity degrades type III capsular polysaccharide of Streptococcus pneumoniae (Spn). This capsular polysaccharide is also known as Pneumococcal type-3 polysaccharide (Pn3P) and is expressed by serotype 3 (also referred to as type 3) S. pneumoniae. The structure of Pn3P is shown in FIG. 1.

Whether a protein has Pn3Pase activity can be determined by in vitro assays. In one embodiment, an in vitro assay is carried out as described herein (see Example 1). Briefly, Pn3P can be labeled with a detectable moiety, exposed to a protein being tested for Pn3Pase activity, and the reaction products resolved using a method that permits detection of differences in molecular weight. Pn3P can be obtained using methods that are known to the skilled person and routine or can be purchased from American Type Culture Collection, ATCC (Manassas, Va.). Methods for detecting changes in molecular weight of polysaccharides are known to the skilled person and are routine.

A Pn3Pase protein can be, and in some embodiments preferably is, a mature protein. In one embodiment, a Pn3Pase protein is encoded by a coding sequence obtained from a wild-type cell where the protein has been processed to remove one or more amino acids from the N-terminal end to result in a mature protein, e.g., the protein lacks a signal sequence. Thus, a mature protein can lack, when compared to a preprocessed Pn3Pase protein encoded by a coding sequence obtained from a wild-type cell, at least one, at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, at least 30, at least 31, at least 32, at least 33, at least 34, at least 35, at least 36, at least 37, at least 38, at least 39, at least 40, at least 41, at least 42, at least 43, at least 44, at least 45, at least 46, at least 47, at least 48, at least 49, at least 50, at least 51, at least 52, at least 53, at least 54, at least 55, at least 56, at least 57, at least 58, at least 59, at least 60, at least 61, at least 62, or at least 63 amino acids from the amino terminus of the preprocessed protein. In another embodiment, a Pn3Pase protein is encoded by a coding region that does not include nucleotides encoding amino acids corresponding to a signal sequence.

An example of a Pn3Pase protein is depicted at SEQ ID NO:2, where the Pn3Pase protein is a preprocessed protein. Examples of a mature Pn3Pase protein include an amino acid sequence having an N-terminal amino acid that is selected from amino acid 2-64 of SEQ ID NO:2 and the C-terminal amino acid is residue 1545 of SEQ ID NO:2. Other examples of Pn3Pase proteins include those having sequence similarity with the amino acid sequence of SEQ ID NO:2 or a mature Pn3Pase protein that includes a subset of amino acids of SEQ ID NO:2. A Pn3Pase protein having sequence similarity with the amino acid sequence of SEQ ID NO:2 or a portion thereof has Pn3Pase activity. A preprocessed or mature Pn3Pase protein may be isolated from a microbe, such as a member of the genera Bacillus, such as B. circulans. A specific example of a microbe is Bacillus circulans Jordan strain 32352 (ATCC 14175). Data from determining the nucleotide sequence of Bacillus circulans indicates this bacterium should be reclassified in the genus Paenibacillus, as its nearest neighbors phylogenetically lie within this classification. Paenibacillus species were previously included within the Bacillus genus until they were deemed appropriately dissimilar (Ash et al., 1993, Antonie Van Leeuwenhoek 64:253-260). Classification into the Paenibacillus genus was confirmed by the presence of the unique group 3 bacilli (Paenibacilli) nucleotide sequence (TCGATACCCTTGGTGCCGAAGT, SEQ ID NO:3) on 16s ribosomal RNA (Ash et al., 1993, Antonie Van Leeuwenhoek 64:253-260). A Pn3Pase protein can also be produced using recombinant techniques, or chemically or enzymatically synthesized using routine methods. A recombinantly-produced protein may include the entire amino acid sequence translatable from an mRNA transcript, or a portion thereof that encodes a mature Pn3Pase protein.

The amino acid sequence of a Pn3Pase protein having sequence similarity to SEQ ID NO:2 or a portion thereof corresponding to a mature Pn3Pase protein may include conservative substitutions of amino acids. A conservative substitution is typically the substitution of one amino acid for another that is a member of the same class. For example, it is well known in the art of protein biochemistry that an amino acid belonging to a grouping of amino acids having a particular size or characteristic (such as charge, hydrophobicity, and/or hydrophilicity) may generally be substituted for another amino acid without substantially altering the secondary and/or tertiary structure of a protein. For the purposes of this disclosure, conservative amino acid substitutions are defined to result from exchange of amino acids residues from within one of the following classes of residues: Class I: Gly, Ala, Val, Leu, and Ile (representing aliphatic side chains); Class II: Gly, Ala, Val, Leu, Ile, Ser, and Thr (representing aliphatic and aliphatic hydroxyl side chains); Class III: Tyr, Ser, and Thr (representing hydroxyl side chains); Class IV: Cys and Met (representing sulfur-containing side chains); Class V: Glu, Asp, Asn and Gln (carboxyl or amide group containing side chains); Class VI: His, Arg and Lys (representing basic side chains); Class VII: Gly, Ala, Pro, Trp, Tyr, Ile, Val, Leu, Phe and Met (representing hydrophobic side chains); Class VIII: Phe, Trp, and Tyr (representing aromatic side chains); and Class IX: Asn and Gln (representing amide side chains). The classes are not limited to naturally occurring amino acids, but also include artificial amino acids, such as beta or gamma amino acids and those containing non-natural side chains, and/or other similar monomers such as hydroxyacids.

Guidance concerning how to make phenotypically silent amino acid substitutions is provided in Bowie et al. (1990, Science, 247:1306-1310), wherein the authors indicate proteins are surprisingly tolerant of amino acid substitutions. For example, Bowie et al. disclose that there are two main approaches for studying the tolerance of a protein sequence to change. The first method relies on the process of evolution, in which mutations are either accepted or rejected by natural selection. The second approach uses genetic engineering to introduce amino acid changes at specific positions of a cloned gene and selects or screens to identify sequences that maintain functionality. As stated by the authors, these studies have revealed that proteins are surprisingly tolerant of amino acid substitutions. The authors further indicate which changes are likely to be permissive at a certain position of the protein. For example, most buried amino acid residues require non-polar side chains, whereas few features of surface side chains are generally conserved. Other such phenotypically silent substitutions are described in Bowie et al, and the references cited therein.

Guidance on how to modify the amino acid sequences of proteins disclosed herein is also provided at FIG. 2. FIG. 2 depicts a Clustal Omega amino acid alignment of glycoside hydrolase proteins expressed by Paenibacillus. Clustal Omega is a multiple sequence alignment program (Sievers et al., 2011, Molecular Systems Biology 7: 539, doi:10.1038/msb.2011.75; Goujon et al., 2010, Nucleic acids research 38 (Suppl 2):W695-9, doi:10.1093/nar/gkq313). In FIG. 2 an asterisk (*) indicates positions which have a single, fully conserved residue; a colon (:) indicates conservation between groups of strongly similar properties, roughly equivalent to scoring >0.5 in the Gonnet PAM 250 matrix; a period (.) indicates conservation between groups of weakly similar properties, roughly equivalent to scoring=<0.5 and >0 in the Gonnet PAM 250 matrix. By reference to this figure, the skilled person can predict which alterations to an amino acid sequence are likely to modify enzymatic activity, as well as which alterations are unlikely to modify enzymatic activity.

Pn3Pase proteins include conserved domains including a glycoside hydrolase, family 39 domain (amino acids 180-353 of SEQ ID NO:2), galactose-binding domain-like (amino acids 621-765 of SEQ ID NO:2), a domain of unknown function DUF1080 (amino acids 781-950 of SEQ ID NO:2) with structural similarity to an endo-1,3-1,4-beta glucanase, and a concanavalin A-like lectin/glucanase domain (amino acids 1,209-1,348 of SEQ ID NO:2). In one embodiment, a Pn3Pase protein has the characteristic of displaying slightly better activity in sodium phosphate buffer at pH 7.2 than in MES buffer pH 6.0, and significantly worse in Tris buffer at pH 8.0 (see example 1). In another embodiment, a Pn3Pase protein displays a concentration-dependent preference for Ca2+, as it produces a higher concentration of reducing end GlcA in presence of 10 mM Ca2+(see example 1).

A Pn3Pase protein described herein can be expressed as a fusion protein that includes a Pn3Pase protein described herein and heterologous amino acids. For instance, the additional amino acid sequence may be useful for purification of the fusion protein by affinity chromatography. Amino acid sequences useful for purification can be referred to as a tag, and include but are not limited to a polyhistidine-tag (His-tag) and maltose-binding protein. Representative examples may be found in Hopp et al. (U.S. Pat. No. 4,703,004), Hopp et al. (U.S. Pat. No. 4,782,137), Sgarlato (U.S. Pat. No. 5,935,824), and Sharma Sgarlato (U.S. Pat. No. 5,594,115). Various methods are available for the addition of such affinity purification moieties to proteins. Optionally, the additional amino acid sequence, such as a His-tag, can then be cleaved.

Polynucleotides

Also provided herein are isolated polynucleotides encoding a Pn3Pase protein. A polynucleotide encoding a protein having Pn3Pase activity is referred to herein as a Pn3Pase polynucleotide. Pn3Pase polynucleotides may have a nucleotide sequence encoding a protein having the amino acid sequence shown in SEQ ID NO:2, or a portion thereof. An example of the class of nucleotide sequences encoding such a protein is SEQ ID NO:1 or a portion thereof. It should be understood that a polynucleotide encoding a Pn3Pase protein represented by SEQ ID NO:2 is not limited to the nucleotide sequence disclosed at SEQ ID NO:1, but also includes the class of polynucleotides encoding such proteins as a result of the degeneracy of the genetic code. For example, the naturally occurring nucleotide sequence SEQ ID NO:1 is but one member of the class of nucleotide sequences encoding a protein having the amino acid sequence SEQ ID NO:2. The class of nucleotide sequences encoding a selected protein sequence is large but finite, and the nucleotide sequence of each member of the class may be readily determined by one skilled in the art by reference to the standard genetic code, wherein different nucleotide triplets (codons) are known to encode the same amino acid.

A Pn3Pase polynucleotide may have sequence similarity with the nucleotide sequence of SEQ ID NO:1 or a portion thereof, for instance nucleotides encoding a mature Pn3Pase protein. Pn3Pase polynucleotides having sequence similarity with the nucleotide sequence of SEQ ID NO:1, or a portion thereof, encode a Pn3Pase protein. A Pn3Pase polynucleotide may be isolated from a microbe, such as Paenibacillus sp., or may be produced using recombinant techniques, or chemically or enzymatically synthesized. A Pn3Pase polynucleotide may further include heterologous nucleotides flanking the open reading frame encoding the Pn3Pase protein. Typically, heterologous nucleotides may be at the 5′ end of the coding region, at the 3′ end of the coding region, or the combination thereof. The number of heterologous nucleotides may be, for instance, at least 10, at least 100, or at least 1000.

A polynucleotide described herein may be present in a vector. A vector is a replicating polynucleotide, such as a plasmid, phage, or cosmid, to which another polynucleotide may be attached so as to bring about the replication of the attached polynucleotide. Construction of vectors containing a polynucleotide of the disclosure employs standard ligation techniques known in the art. See, e.g., Sambrook et al, Molecular Cloning: A Laboratory Manual., Cold Spring Harbor Laboratory Press (1989). A vector may provide for further cloning (amplification of the polynucleotide), i.e., a cloning vector, or for expression of the polynucleotide, i.e., an expression vector. The term vector includes, but is not limited to, plasmid vectors, viral vectors, cosmid vectors, and artificial chromosome vectors. Examples of viral vectors include, for instance, adenoviral vectors, adeno-associated viral vectors, lentiviral vectors, retroviral vectors, and herpes virus vectors. Typically, a vector is capable of replication in a microbial host, for instance, a microbe such as E. coli, or in a eukaryotic host, for instance, a yeast cell, a mammalian cell, or an insect cell. In one embodiment the vector is a plasmid.

Selection of a vector depends upon a variety of desired characteristics in the resulting construct, such as a selection marker, vector replication rate, and the like. In some aspects, suitable host cells for cloning or expressing the vectors herein include prokaryotic cells. Vectors may be introduced into a host cell using methods that are known and used routinely by the skilled person. For example, calcium phosphate precipitation, electroporation, heat shock, lipofection, microinjection, and viral-mediated nucleic acid transfer are common methods for introducing nucleic acids into host cells.

Polynucleotides encoding a Pn3Pase protein may be obtained from microbes, for instance, a microbe, such as Paenibacillus sp., or produced in vitro or in vivo. For instance, methods for in vitro synthesis include, but are not limited to, chemical synthesis with a conventional DNA/RNA synthesizer. Commercial suppliers of synthetic polynucleotides and reagents for such synthesis are well known.

An expression vector optionally includes regulatory sequences operably linked to the coding region. The disclosure is not limited by the use of any particular promoter, and a wide variety of promoters are known. Promoters act as regulatory signals that bind RNA polymerase in a cell to initiate transcription of a downstream (3′ direction) coding region. The promoter used may be a constitutive or an inducible promoter. It may be, but need not be, heterologous with respect to the host cell. The promoter useful in methods described herein may be, but is not limited to, a constitutive promoter, a temperature sensitive promoter, a non-regulated promoter, or an inducible promoter. In one embodiment, a promoter is one that functions in a member of the domain Bacteria. In one embodiment, a promoter is one that functions in a eukaryote.

An expression vector may optionally include a ribosome binding site and a start site (e.g., the codon ATG) to initiate translation of the transcribed message to produce the protein. It may also include a termination sequence to end translation. A termination sequence is typically a codon for which there exists no corresponding aminoacetyl-tRNA, thus ending protein synthesis. The polynucleotide used to transform the host cell may optionally further include a transcription termination sequence.

A vector introduced into a host cell to result in a genetically modified cell optionally includes one or more marker sequences, which typically encode a molecule that inactivates or otherwise detects or is detected by a compound in the growth medium. For example, the inclusion of a marker sequence may render the transformed cell resistant to an antibiotic, or it may confer compound-specific metabolism on the transformed cell. Examples of a marker sequence include, but are not limited to, sequences that confer resistance to kanamycin, ampicillin, chloramphenicol, tetracycline, streptomycin, and neomycin.

Proteins described herein may be produced using recombinant DNA techniques, such as an expression vector present in a cell. Such methods are routine and known in the art. The proteins may also be synthesized in vitro, e.g., by solid phase peptide synthetic methods. The solid phase peptide synthetic methods are routine and known in the art. A protein produced using recombinant techniques or by solid phase peptide synthetic methods may be further purified by routine methods, such as fractionation on immunoaffinity or ion-exchange columns, ethanol precipitation, reverse phase HPLC, chromatography on silica or on an anion-exchange resin such as DEAE, chromatofocusing, SDS-PAGE, ammonium sulfate precipitation, gel filtration using, for example, Sephadex G-75, or ligand affinity.

Genetically Modified Cells

Also provided is a genetically modified cell having a polynucleotide encoding a Pn3Pase described herein. Compared to a control cell that is not genetically modified, a genetically modified cell can exhibit production of a Pn3Pase, or can exhibit increased production of a Pn3Pase. A polynucleotide encoding a Pn3Psae may be present in the cell as a vector or integrated into genomic DNA, such as a chromosome or a plasmid, of the genetically modified cell. A cell can be a eukaryotic cell or a prokaryotic cell, such as a member of the domain Bacteria

Examples of host cells that are members of the domain Bacteria that can be genetically modified to include a polynucleotide encoding a Pn3Pase described herein include, but are not limited to, Escherichia (such as Escherichia coli), and Salmonella (such as Salmonella enterica, Salmonella typhi, Salmonella typhimurium).

Examples of host cells that are eukaryotic cells that can be genetically modified to include a polynucleotide encoding a Pn3Pase include, but are not limited to, yeast such as Saccharomyces cerevisiae and Pichia spp., insect cells, and mammalian cells.

Compositions

Also provided are compositions that include a Pn3Pase protein described herein or a polynucleotide encoding a Pn3Pase protein. Such compositions typically include a pharmaceutically acceptable carrier. As used herein “pharmaceutically acceptable carrier” includes saline, solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with pharmaceutical administration. Additional active agents can also be incorporated into the compositions.

A composition may be prepared by methods well known in the art of pharmaceutics. In general, a composition can be formulated to be compatible with its intended route of administration. Administration may be systemic or local. Examples of routes of administration include parenteral (e.g., intravenous, intradermal, subcutaneous, intraperitoneal, intramuscular), enteral (e.g., oral), and topical (e.g., epicutaneous, inhalational, transmucosal) administration. Appropriate dosage forms for enteral administration of the compound of the present disclosure include, but are not limited to, tablets, capsules or liquids. Appropriate dosage forms for parenteral administration may include intravenous or intraperitoneal administration. Appropriate dosage forms for topical administration include, but are not limited to, nasal sprays, metered dose inhalers, dry-powder inhalers or by nebulization.

Solutions or suspensions can include the following components: a sterile diluent such as water for administration, saline solution, fixed oils, polyethylene glycols, glycerin, propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates; electrolytes, such as sodium ion, chloride ion, potassium ion, calcium ion, and magnesium ion, and agents for the adjustment of tonicity such as sodium chloride or dextrose. pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide.

Compositions can include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile solutions or dispersions. For parenteral administration, suitable carriers include physiological saline, bacteriostatic water, phosphate buffered saline (PBS), and the like. A composition is typically sterile and, when suitable for injectable use, should be fluid to the extent that easy syringability exists. It should be stable under the conditions of manufacture and storage and preserved against the contaminating action of microorganisms such as bacteria and fungi. The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyetheylene glycol, and the like), and suitable mixtures thereof. Prevention of the action of microorganisms can be achieved by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, ascorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars, polyalcohols such as mannitol, sorbitol, sodium chloride in the composition. Prolonged absorption of the injectable compositions can be brought about by including in the composition an agent which delays absorption, for example, aluminum monostearate and gelatin.

Sterile solutions can be prepared by incorporating the active compound (e.g., a Pn3Pase protein described herein or a polynucleotide encoding the protein) in the required amount in an appropriate solvent with one or a combination of ingredients routinely used in pharmaceutical compositions, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the active compound into a sterile vehicle, which contains a basic dispersion medium and any other appropriate ingredients. In the case of sterile powders for the preparation of sterile injectable solutions, preferred methods of preparation include vacuum drying and freeze-drying which yields a powder of the active ingredient plus any additional desired ingredient from a previously sterilized solution thereof.

Oral compositions generally include an inert diluent or an edible carrier. For the purpose of oral therapeutic administration, the active compound can be incorporated with excipients and used in the form of tablets, troches, or capsules, e.g., gelatin capsules. Oral compositions can also be prepared using a fluid carrier. Pharmaceutically compatible binding agents and/or other useful materials can be included as part of the composition. The tablets, pills, capsules, troches and the like can contain any of the following ingredients, or compounds of a similar nature: a binder such as microcrystalline cellulose, gum tragacanth or gelatin; an excipient such as starch or lactose, a disintegrating agent such as alginic acid, Primogel, or corn starch; a lubricant such as magnesium stearate or Sterotes; a glidant such as colloidal silicon dioxide; a sweetening agent such as sucrose or saccharin; or a flavoring agent such as peppermint, methyl salicylate, or orange flavoring.

For administration by inhalation (e.g., topical administration), the active compounds can be delivered in the form of an aerosol spray from a pressured container or dispenser which contains a suitable propellant, e.g., a gas such as carbon dioxide, or a nebulizer.

Systemic administration can also be by transmucosal or transdermal means. For transmucosal or transdermal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art, and include, for example, for transmucosal administration, detergents, bile salts, and fusidic acid derivatives. Transmucosal administration can be accomplished through the use of nasal sprays or suppositories. For transdermal administration, the active compounds are formulated into ointments, salves, gels, or creams as generally known in the art.

In those embodiments where a polynucleotide encoding a recombinant protein is administered, any method suitable for administration of polynucleotide agents can be used, such as gene guns, bio injectors, and skin patches as well as needle-free methods such as micro-particle DNA vaccine technologies (Johnston et al., U.S. Pat. No. 6,194,389).

The active compounds may be prepared with carriers that will protect the compound against rapid elimination from the body, such as a controlled release formulation, including implants. Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Such formulations can be prepared using standard techniques. Liposomal suspensions can also be used as pharmaceutically acceptable carriers. These can be prepared according to methods known to those skilled in the art.

Toxicity and therapeutic efficacy of the active compounds can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LD50 (the dose lethal to 50% of the population) and the ED50 (the dose therapeutically effective in 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio LD50/ED50. Recombinant proteins exhibiting high therapeutic indices are preferred.

The data obtained from cell culture assays and animal studies can be used in formulating a range of dosage for use in humans. The dosage of such compounds lies preferably within a range of circulating concentrations that include the ED50 with little or no toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration used. For a compound used in the methods described herein, the therapeutically effective dose can be estimated initially from animal models. A dose may be formulated in animal models to achieve a circulating plasma concentration range that includes the IC50 (i.e., the concentration of the test compound which achieves a half-maximal inhibition of signs of disease, such as obesity). Such information can be used to more accurately determine useful doses in humans. Levels in plasma may be measured using routine methods.

The compositions can be administered one or more times per day to one or more times per week, including once every other day. The skilled artisan will appreciate that certain factors may influence the dosage and timing required to effectively treat a subject, including but not limited to the severity of the condition, previous treatments, the general health and/or age of the subject, and other diseases present. Moreover, treatment of a subject with an effective amount of an active compound can include a single treatment or, preferably, can include a series of treatments.

Methods of Use

Also provided are methods. In one embodiment, a method is for making Pn3Pase protein described herein. In one embodiment, the method includes incubating a cell under suitable conditions for expression of a Pn3Pase protein. The cell can be, but it not limited to, a genetically modified cell or a naturally occurring cell that produces a Pn3Pase protein. An example of a naturally occurring cell is a Paenibacillus strain, such as Paenibacillus sp. 32352. Optionally, the method includes introducing into a host cell a vector that includes a coding region encoding a Pn3Pase protein. In one embodiment, the method includes isolating or purifying the Pn3Pase protein from a cell or from a medium. In those embodiments where the Pn3Pase protein includes additional amino acids useful for isolating or purifying the protein, the method can also include cleavage of the additional amino acids from the Pn3Pase protein.

In one embodiment, a method is for cleaving a Pn3P molecule. In one embodiment, the method includes exposing a Pn3P molecule to a Pn3Pase protein. The P3nP molecule can be part of a Streptococcus pneumoniae microbe, e.g., the Pn3P molecule can be the capsular polysaccharide of an S. pneumoniae, or the Pn3P molecule can be separate from an S. pneumoniae microbe, e.g., the Pn3P molecule can be isolated. In one embodiment, the S. pneumoniae microbe is serotype 3. In one embodiment, the Pn3P molecule is in vivo, and in another embodiment, the Pn3P molecule is in vitro.

In one embodiment, a method is for reducing the amount of type III capsular polysaccharide on the surface of Streptococcus pneumoniae. The method includes contacting a Streptococcus pneumoniae having type III capsular polysaccharide present on its surface with a Pn3Pase protein. The Pn3Pase protein can be isolated or purified, and can be present in a composition. In one embodiment, the contacting can include exposing the microbe to a genetically modified cell that expresses the Pn3Pase protein. The contacting can be under conditions suitable for enzymatic hydrolysis of type III capsular polysaccharide. Optionally, the the Streptococcus pneumoniae with the reduced amount of type III capsular polysaccharide has increased susceptibility to phagocytosis by macrophages, increased complement-mediated killing by neutrophils, or a combination thereof, compared to the Streptococcus pneumoniae that is not contacted with the Pn3Pase protein. In one embodiment, the S. pneumoniae microbe is serotype 3. In one embodiment, the S. pneumoniae microbe is in vivo, and in another embodiment, the S. pneumoniae microbe is in vitro.

In one embodiment, a method is for increasing deposition of at least one complement component on the surface of Streptococcus pneumoniae. The method includes contacting a Streptococcus pneumoniae having type III capsular polysaccharide present on its surface with a Pn3Pase protein. The Pn3Pase protein can be isolated or purified, and can be present in a composition. In one embodiment, the contacting can include exposing the microbe to a genetically modified cell that expresses the Pn3Pase protein. The contacting can be under conditions suitable for enzymatic hydrolysis of type III capsular polysaccharide. In one embodiment, the S. pneumoniae microbe is serotype 3. In one embodiment, the S. pneumoniae microbe is in vivo, and in another embodiment, the S. pneumoniae microbe is in vitro.

In one embodiment, a method includes treating an infection in a subject caused by Streptococcus pneumoniae. The subject used in a method described herein can be an animal such as, but not limited to, a murine (e.g., mouse or rat) or a human. The method includes administering an effective amount of the composition to an animal having an infection caused by Streptococcus pneumoniae. Optionally, the method can include determining whether the Streptococcus pneumoniae causing the infection has decreased. Methods for determining whether an infection is caused by a Streptococcus pneumoniae are routine and known in the art. The infection can be localized or systemic. An example of a localized Streptococcus pneumoniae infection is colonization of the nasal cavity, e.g., the nasopharynx. In one embodiment, topical administration of a composition described herein can be used to reduce nasopharyngeal colonization in a subject. Another example of a localized Streptococcus pneumoniae infection of the lung, e.g., pneumococcal pneumonia. In one embodiment, topical administration of a composition by, for instance, aerosol, can be used to reduce pneumococcal pneumonia in a subject. An example of a systemic Streptococcus pneumoniae infection is the presence of Streptococcus pneumoniae in the blood of a subject (e.g., bacteremia or sepsis). In one embodiment, parenteral administration of a composition can be used to reduce a systemic Streptococcus pneumoniae infection in a subject. In this aspect of the disclosure, an “effective amount” of a composition of the present disclosure is the amount able to elicit the desired response in the recipient, e.g., a reduction in the amount of Streptococcus pneumoniae present in a subject. The reduction can be a reduction in the number of S. pneumoniae in the nasopharynx, lung, or blood of a subject. The reduction can be a decrease of at least 2-fold, at least 3-fold, or at least 4-fold in the subject compared to the subject before administering the composition. In one embodiment, the S. pneumoniae microbe is serotype 3.

In another embodiment, a method includes treating one or more symptoms of certain conditions in animals that may be caused by infection by a Streptococcus pneumoniae. Streptococcus pneumoniae infections cause invasive pneumococcal disease. Examples of conditions caused by invasive pneumococcal disease include pneumonia, pneumococcal meningitis, otitis media, bacteremia, and sepsis. Symptoms associated with these conditions include chills, cough, rapid breathing, difficulty breathing, chest pain (pneumonia), stiff neck, fever, headache, confusion and photophobia (pneumococcal meningitis), and confusion, shortness of breath, elevated heart rate, pain or discomfort, over-perspiration, fever, and shivering (sepsis). In one embodiment, the S. pneumoniae microbe is serotype 3.

Treatment of one or more of these conditions can be prophylactic or, alternatively, can be initiated after the development of a condition described herein. Treatment that is prophylactic, for instance, initiated before a subject manifests a symptom of a condition caused by Streptococcus pneumoniae, is referred to herein as treatment of a subject that is “at risk” of developing the condition. Typically, an animal “at risk” of developing a condition is an animal likely to be exposed to a Streptococcus pneumoniae causing the condition. Accordingly, administration of a composition can be performed before, during, or after the occurrence of the conditions described herein. Treatment initiated after the development of a condition may result in decreasing the severity of the symptoms of one of the conditions, including completely removing the symptoms. In this aspect of the disclosure, an “effective amount” is an amount effective to prevent the manifestation of symptoms of a condition, decrease the severity of the symptoms of a condition, and/or completely remove the symptoms. In one embodiment, the S. pneumoniae microbe is serotype 3.

The potency of a composition described herein can be tested according to standard methods. For instance, the use of mice as an experimental model for Streptococcus pneumoniae infection in humans is well established.

Kits

The present disclosure also provides a kit for making a Pn3Pase protein. In one embodiment, the kit includes a vector that includes a coding region encoding a Pn3Pase protein in an amount sufficient for transforming a cell. In one embodiment, the kit includes a genetically modified cell that includes a coding region encoding a Pn3Pase protein in a suitable packaging material.

In another embodiment, the present disclosure also provides a kit directed to using a Pn3Pase protein. In one embodiment, the kit includes Pn3Pase protein, isolated or optionally purified, in a suitable packaging material.

Optionally, other reagents such as buffers or a pharmaceutically acceptable carrier (either prepared or present in its constituent components, where one or more of the components may be premixed or all of the components may be separate), and the like, are also included. In one embodiment, the protein, vector, or genetically modified cell may be present with a buffer, or may be present in separate containers. Instructions for use of the packaged components are also typically included.

As used herein, the phrase “packaging material” refers to one or more physical structures used to house the contents of the kit. The packaging material is constructed by known methods, preferably to provide a sterile, contaminant-free environment. The packaging material has a label, which indicates that the contents can be used for transforming a cell or producing Pn3Pase protein. In addition, the packaging material contains instructions indicating how the materials within the kit are used. As used herein, the term “package” refers to a solid matrix or material such as glass, plastic, paper, foil, and the like, capable of holding within fixed limits a vector or a genetically modified cell. Thus, for example, a package can include a glass or plastic vial used to contain appropriate quantities of a Pn3Pase protein. “Instructions for use” typically include a tangible expression describing the reagent concentration or at least one method parameter.

ILLUSTRATIVE ASPECTS

Aspect 1. A genetically modified cell comprising a mature Pn3Pase protein, wherein the protein has Pn3Pase activity.

Aspect 2. A genetically modified cell comprising a polynucleotide comprising a coding region, wherein the coding region comprises a nucleotide sequence encoding a mature Pn3Pase protein, and wherein the protein has Pn3Pase activity.

Aspect 3. The genetically modified cell of Aspect 1 or 2 wherein the protein comprises an amino acid sequence having at least 80% identity with an amino acid sequence selected from SEQ ID NO:2, wherein the amino terminal amino acid is selected from any one of residues 2 to 64 of SEQ ID NO:2 and the carboxy terminal amino acid is residue 1545 of SEQ ID NO:2.

Aspect 4. The genetically modified cell of any one of Aspects 1-3 wherein the protein comprises an amino acid sequence having at least 80% identity with amino acids 41-1545 of SEQ ID NO:2.

Aspect 5. The genetically modified cell of any one of Aspects 1-4 wherein the cell is a eukaryotic cell.

Aspect 6. The genetically modified cell of any one of Aspects 1-5 wherein the cell is a mammalian cell, a yeast cell, or an insect cell.

Aspect 7. The genetically modified cell of any one of Aspects 1-6 wherein the cell is a prokaryotic cell.

Aspect 8. The genetically modified cell of any one of Aspects 1-7 wherein the cell is E. coli.

Aspect 9. The genetically modified cell of any one of Aspects 1-8 wherein the protein comprises a heterologous amino acid sequence.

Aspect 10. The genetically modified cell of any one of Aspects 1-9 wherein the heterologous amino acid sequence comprises a tag.

Aspect 11. A composition comprising the genetically modified cell of any one of Aspects 1-10.

Aspect 12. A composition comprising an isolated mature P3nPase protein, wherein the protein has Pn3Pase activity.

Aspect 13. The composition of any one of Aspects 1-12 wherein the protein is purified.

Aspect 14. A composition comprising an isolated polynucleotide, wherein the polynucleotide comprises a coding region encoding a mature Pn3Pase protein, and wherein the protein has Pn3Pase activity.

Aspect 15. The composition of any one of Aspects 12-14 wherein the protein comprises an amino acid sequence having at least 80% identity with an amino acid sequence selected from SEQ ID NO:2, wherein the amino terminal amino acid is selected from residues 2 to 64 of SEQ ID NO:2 and the carboxy terminal amino acid is residue 1545 of SEQ ID NO:2.

Aspect 16. The composition of any one of Aspects 12-15 wherein the protein comprises an amino acid sequence having at least 80% identity with amino acids 41-1545 of SEQ ID NO:2.

Aspect 17. The composition of any one of Aspects 11-16 wherein the composition comprises a pharmaceutically acceptable carrier.

Aspect 18. A method comprising: incubating a cell under conditions suitable for expression of a protein having Pn3Pase activity, wherein the cell comprises a polynucleotide comprising a coding region, wherein the coding region comprises a nucleotide sequence encoding a mature Pn3Pase protein, wherein the protein has Pn3Pase activity, and wherein the cell expresses the mature Pn3Pase protein.

Aspect 19. The method of Aspect 18 wherein the protein comprises an amino acid sequence having at least 80% identity with an amino acid sequence selected from SEQ ID NO:2, wherein the amino terminal amino acid is selected from any one of residues 2 to 64 of SEQ ID NO:2 and the carboxy terminal amino acid is residue 1545 of SEQ ID NO:2.

Aspect 20. The method of any one of Aspects 18-19 wherein the protein comprises an amino acid sequence having at least 80% identity with amino acids 41-1545 of SEQ ID NO:2.

Aspect 21. The method of any one of Aspects 18-20 wherein the cell is a genetically modified cell and the polynucleotide is an exogenous polynucleotide.

Aspect 22. The method of any one of Aspects 18-21 further comprising isolating the protein.

Aspect 23. The method of any one of Aspects 18-21 further comprising purifying the protein.

Aspect 24. The method of any one of Aspects 18-21 wherein the cell is a eukaryotic cell.

Aspect 25. The method of any one of Aspects 18-24 wherein the cell is a mammalian cell, a yeast cell, or an insect cell.

Aspect 26. The method of any one of Aspects 18-25 wherein the cell is a prokaryotic cell.

Aspect 27. The method of any one of Aspects 18-26 wherein the prokaryotic cell is E. coli.

Aspect 28. The method of any one of Aspects 18-27 wherein the protein comprises a heterologous amino acid sequence.

Aspect 29. The method of any one of Aspects 18-28 wherein the heterologous amino acid sequence comprises a tag.

Aspect 30. A method comprising:

-   -   contacting a Streptococcus pneumoniae comprising a type III         capsular polysaccharide with a mature Pn3Pase protein comprising         Pn3Pase activity, wherein the contacting is under conditions         suitable for enzymatic hydrolysis of type III capsular         polysaccharide, wherein the amount of type III capsular         polysaccharide on the surface of the S. pneumoniae is reduced         compared to the S. pneumoniae that is not contacted with the         Pn3Pase protein.

Aspect 31. A method for increasing deposition of at least one complement component on the surface of a Streptococcus pneumoniae, the method comprising:

contacting a Streptococcus pneumoniae comprising a type III capsular polysaccharide with a mature Pn3Pase protein comprising Pn3Pase activity, wherein the deposition of at least one complement component on the surface of the S. pneumoniae is increased compared to the S. pneumoniae that is not contacted with the Pn3Pase protein.

Aspect 32. The method of Aspect 30 or 31 wherein the protein comprises an amino acid sequence having at least 80% identity with an amino acid sequence selected from SEQ ID NO:2, wherein the amino terminal amino acid is selected from any one of residues 2 to 64 of SEQ ID NO:2 and the carboxy terminal amino acid is residue 1545 of SEQ ID NO:2.

Aspect 33. The method of any one of Aspects 30-32 wherein the protein comprises an amino acid sequence having at least 80% identity with amino acids 41-1545 of SEQ ID NO:2.

Aspect 34. The method of any one of Aspects 30-33 wherein the S. pneumoniae is present in conditions suitable for replication of the S. pneumoniae.

Aspect 35. The method of any one of Aspects 30-34 wherein the mature Pn3Pase protein is an isolated Pn3Pase protein.

Aspect 36. The method of any one of Aspects 30-35 wherein the contacting comprises exposing the S. pneumoniae to a genetically modified cell that expresses the mature Pn3Pase protein.

Aspect 37. The method of any one of Aspects 30-36 wherein the S. pneumoniae has increased susceptibility to phagocytosis by macrophages, increased complement-mediated killing by neutrophils, or a combination thereof, compared to the S. pneumoniae that is not contacted with the Pn3Pase protein.

Aspect 38. The method of any one of Aspects 30-37 wherein the S. pneumoniae is present in a subject.

Aspect 39. A method for treating an infection in a subject, the method comprising:

-   -   administering an effective amount of a composition comprising a         mature Pn3Pase protein having Pn3Pase activity to a subject         having or at risk of having an infection caused by a serotype         3 S. pneumoniae.

Aspect 40. A method for treating a symptom in a subject, the method comprising:

administering an effective amount of a composition comprising a mature Pn3Pase protein having Pn3Pase activity to a subject having or at risk of having an infection caused by a serotype 3 S. pneumoniae.

Aspect 41. A method for decreasing colonization in a subject, the method comprising:

administering an effective amount of a composition comprising a comprising a mature Pn3Pase protein having P3nPase activity to a subject colonized by or at risk of being colonized by a serotype 3 S. pneumoniae.

Aspect 42. The method of any one of Aspects 39-41 wherein the protein comprises an amino acid sequence having at least 80% identity with an amino acid sequence selected from SEQ ID NO:2, wherein the amino terminal amino acid is selected from any one of residues 2 to 64 of SEQ ID NO:2 and the carboxy terminal amino acid is residue 1545 of SEQ ID NO:2.

Aspect 43. The method of any one of Aspects 39-42 wherein the protein comprises an amino acid sequence having at least 80% identity with amino acids 41-1545 of SEQ ID NO:2.

Aspect 44. The method of any one of Aspects 39-43 wherein the subject is a human.

Aspect 45. A mature Pn3Pase protein disclosed herein for use in therapy.

Aspect 46. A mature Pn3Pase protein disclosed herein for use as a medicament.

Aspect 47. A mature Pn3Pase protein disclosed herein for use in the treatment of a condition.

Aspect 48. Use of a mature Pn3Pase protein disclosed herein for preparation of a medicament for the treatment of pneumonia, pneumococcal meningitis, otitis media, bacteremia, sepsis, or a combination thereof.

Aspect 49. The composition comprising a mature P3nPase protein described herein for use in treating or preventing an infection or a symptom caused by a serotype 3 S. pneumoniae.

Aspect 50. A protein, composition, or method including one or more features described herein.

EXAMPLES

The present invention is illustrated by the following examples. It is to be understood that the particular examples, materials, amounts, and procedures are to be interpreted broadly in accordance with the scope and spirit of the invention as set forth herein.

Example 1 Identification of the Streptococcus pneumoniae Type 3 Capsule-Specific Glycosyl Hydrolase Gene of Paenibacillus sp. 32352 Abstract

‘Bacillus circulans Jordan 32352’ was isolated from decaying organic matter in the New Jersey soil in the early 1930s. This soil-dwelling bacterium produced an enzyme capable of degrading the type 3 capsular polysaccharide (Pn3P) of Streptococcus pneumoniae (Spn). Early reports of this enzyme (Pn3Pase) demonstrated its inducibility by, and specificity for Pn3P. A number of studies since have employed Pn3Pase while investigating Pn3P biosynthesis and its antigenic properties. We set out to clone this enzyme for recombinant expression. We first sequenced the genome of this bacterial species and reclassified the Pn3Pase producing bacterium as “Paenibacillus sp. 32352”. Here, we identified the gene of Pn3Pase through mass spectrometry-based proteomics. We cloned the gene for recombinant expression and characterized the oligosaccharide products generated upon the enzymatic depolymerization of Pn3P. We examined the effects of Pn3Pase on live, growing type 3 Spn, so that it may be investigated as a potential therapeutic agent against this hypervirulent serotype of Spn.

In 1930, Avery and Dubos isolated an organism from soil taken from cranberry bogs, which was capable of depolymerizing type 3 capsular polysaccharide of Streptococcus pneumoniae (Pn3P), a linear polymer of −3βGlcA(1-4)βGlc(1-(1,2). The expression of this enzyme (Pn3Pase) was inducible in the presence of Pn3P, and the bacterium was able to grow with Pn3P as the sole carbon source. They described this bacterium as a sporulating, gram-negative, aerobic bacillus with peritrichous flagella. A few years later, Sickles and Shaw isolated two additional similar strains demonstrating the same enzymatic activity targeting Pn3P (3,4). These strains were designated as Bacillus palustris, before being accepted as synonymous to Bacillus circulans (4-6). Besides Pn3Pase, these strains demonstrated the ability to produce enzymes capable of depolymerizing S. pneumoniae capsular serotypes 2 and 8, although soluble protein in cell free extracts were inactive against these polysaccharides (3,7). There are numerous possible practical applications for these strains and enzymes. For example, investigators have applied the Sickles and Shaw Pn3Pase enzyme while examining Pn3P biosynthesis as well as its antigenic and immunological properties (8-11).

We obtained the ‘Bacillus Circulans Jordan strain 32352’ (i.e., the Sickles and Shaw strain) from American Type Culture Collection, and sequenced its genome (12). 16S rRNA analysis revealed that this bacterium belonged in the Paenibacillae genus, and it is now identified as Paenibacillus sp. 32352 (Pbac). Paenibacillus species are of growing interest since the genus was established in 1991 (13). These microbes are a rich source of extracellular enzymes that catalyze a variety of reactions, which have demonstrated utility in numerous agricultural and medical applications (14-19). Database for carbohydrate-active enzyme annotation (dbCAN) of the Paenibacillus sp. 32352 genome indicates 665 carbohydrate active entries out of 7200 predicted genes, 252 of those exhibiting glycosyl hydrolase- or polysaccharide lyase-like architecture (20).

We set out to determine the identity of the gene producing Pn3Pase in order to express and utilize the enzyme's unique Pn3P-specific activity. We postulated the potential use of this enzyme as a therapeutic agent for serotype 3 S. pneumoniae infections. The capsular polysaccharide (CPS) is a major virulence factor for type 3 strains, as non-encapsulated mutants fail to colonize (21). The virulence mechanisms of CPS is to help Spn evade the immune system through resisting or inhibiting its phagocytosis by host macrophages while also limiting mucus-mediated clearance (22). The Pn3P component of the current 13-valent vaccine (PCV13) induces variable immune responses to serotype 3 (23,24). Individuals vaccinated with PCV13 require higher opsonophagocytosis assay serum titers for serotype 3 in comparison with other serotypes (25). Despite current vaccination programs against Spn, it remains one of the world's most lethal pathogens. In addition to vaccination and antibiotic delivery, alternative therapeutic approaches must be considered for fighting these and other encapsulated pathogens.

Described here is the identification of the Paenibacillus Pn3Pase through proteomics of culture supernatant preparations with Pn3P supplemented minimal media growth. We have cloned the Pn3Pase gene and expressed active enzyme in E. coli. We have characterized oligosaccharide products, and optimized conditions for Pn3P depolymerization. We assessed the ability of the enzyme to degrade the capsule on a live virulent type 3 Spn strain to begin investigating Pn3Pase as a potential therapeutic agent.

Results

Pn3P Utilization Induces Expression of Genes Organized into Locus

We began by culturing Pbac in minimal M9 media with either 2% glucose or Pn3P as the sole carbon source. Pbac growth was monitored for 14 h by OD 600 nm to achieve maximum Pn3Pase production, (FIG. 3A). Pbac was able to grow and utilize Pn3P and glucose, but was unable to utilize cellulose. Supernatants from these cultures were concentrated 20×, and proteins were visualized by coomassie staining. In the Pn3P growth conditions a prominent band ˜55 kDa was observed (FIG. 3B). Proteomic analysis of these samples by in-solution trypsin digestion and LC-MS identified numerous proteins that were present in both samples. Two proteins, however, were significantly enriched in the Pn3P growth condition as highlighted in Table 1.

TABLE 1 Proteomic identification of culture supernatant proteins of Paenibacillus sp. 32352 grown in Pn3P. Highlighted are proteins unique to Pn3P grown culture. Gene Description Score Coverage # Unique Peptides # PSMs #AAs MW [kDa] Pbac_3554 *Lipoprotein 1301.24 82.02 49 597 506 55.9 Pbac_1521 Ig-like, group 2, Surface layer protein 450.46 50.17 44 218 1190 128.7 Pbac_6539 Hypothetical protein 237.19 31.20 17 82 577 64.1 Pbac_5871 NLP/P60 family protein 103.53 61.54 6 35 156 16.9 Pbac_1659 Alpha/beta hydrolase fold (EC 3.8.1.5) 94.98 66.07 13 72 280 30.1 Pbac_3551 Hypothetical protein 39.14 16.70 6 53 1545 168.0 NCBI ref seq: WP_079915027

These two Pn3P induced Pbac proteins appear to be organized into a locus of Pn3P utilization (FIG. 3C) consisting of ABC-type polysaccharide transport system, permease component (Pbac_3556), probable ABC transporter permease protein ytcP (Pbac_3555), lipoprotein (Pbac_3554), DNA-binding response regulator, AraC family (Pbac_3553), multidomain protein with s-layer homology region, glug motif, ig motif (Pbac_3552), and hypothetical protein (Pbac_3551). Since two of these proteins are more abundant in the Pn3P growth conditions, we compared the transcription of three genes of this locus with the commonly expressed surface layer protein (Pbac_1521) in the glucose and Pn3P samples by RT-PCR. The transcription of genes 3551, 3552, and 3554 increase ˜130-fold with Pn3P utilization, while mRNA expression of Pbac_1521 is unchanged between the two conditions (FIG. 3D).

Pn3Pase Identification and Domain Analysis

Pbac_3554, Pbac_3552, and Pbac_3551 were cloned and expressed in E. coli BL21 (DE3) cells to determine which upregulated gene product was responsible for Pn3P depolymerase activity. The hypothetical protein Pbac_3551 (Accession WP_079915027), with primary amino acid sequence shown in FIG. 4A, demonstrated rapid and efficient hydrolysis of tritium radio-isotope labeled Pn3P, as shown by counts per minute shift to lower molecular weight oligosaccharides when reaction products were separated by size exclusion chromatography (FIG. 4B). Reactions of recombinant Pn3Pase with unlabeled Pn3P were performed, spotted on a PVDF membrane, and probed with a Pn3P monoclonal antibody. Reactivity to the monoclonal antibody was completely abolished after 4 h Pn3Pase treatment of Pn3P (FIG. 4C).

The translated protein sequence of Pbac_3551 is 1,545 amino acids. Predicted cleavage of the signal peptide by SignalP 4.1 server (26) from residues 1-40 would yield a mature protein of 164.1 kDa. Protein sequence analysis and classification by InterPro online software (27) recognized homology to glycoside hydrolase, family 39 from amino acids 180-353, galactose-binding domain-like from 621-765, a domain of unknown function DUF1080 from 781-950 with structural similarity to an endo-1,3-1,4-beta glucanase, and a concanavalin A-like lectin/glucanase domain from 1,209-1,348 (FIG. 4D). Although segments of this enzyme display some homology to numerous carbohydrate active proteins, no overall homology to known glycosyl hydrolase families across the length of the enzyme exist.

Characterization of Oligosaccharide Products

The oligosaccharide products of Pn3Pase hydrolysis were separated by size exclusion chromatography. This hydrolysis yielded two major product peaks eluting late in the Superdex peptide column corresponding to a tetrasaccharide and hexasaccharide (FIGS. 5A-C). The identities of these peaks were confirmed as tetrasaccharide (FIG. 5B) and hexasaccharide (FIG. 5C) by electrospray ionization mass spectrometry. Mass spectrometry data is summarized in Table 2.

TABLE 2 Different charge states of the tetrasaccharide and hexasaccharide detected by mass spectrometry. m/z observed Charge state Experimental M Theoretical M Error (ppm) Tetrasaccharide 693.1699 1 694.1777 694.1804 −3.85 346.0811 2 694.1779 694.1804 −3.66 Hexasaccharide 1031.2563 1 1032.2641 1032.2653 −1.13 515.1256 2 1032.2669 1032.2653 1.51

The characterization of oligosaccharide products by NMR spectroscopy is presented in FIG. 6. All anomeric proton signals are assigned in representative ¹H NMR spectra of tetra- and hexa-saccharides (FIG. 6). Anomeric proton signals of residue A, C and E at ˜4.70 ppm were overlapped with HOD peak (FIGS. 6A, 4D) but showed up in 2D HSQC spectrum (FIGS. 6B, E). The ³J_(HH) coupling constants of B-1 and D-1 were 8.22 Hz, demonstrating β-linkages. The signals at 5.15 (³J_(HH)=3.69) and 4.58 (³J_(HH)=8.05) ppm correspond to α- and β-configuration of GlcA residue F, respectively. By combining HSQC and COSY experiments (FIGS. 6C, F), we were able to identify that proton signal of F-5 possessed a high chemical shift (˜4.05 ppm) suggesting that GlcA residue (F) was at the reducing end of the carbohydrate chain. These data demonstrate that Pn3Pase cleaves the β(1-4) linkage between glucuronic acid and glucose in the polysaccharide chain.

Pn3Pase Activity Analysis

A time course experiment was performed using tritiated Pn3P and the recombinant Pn3Pase to understand whether this enzymatic degradation proceeds through endolytic or exolytic cleavage. Reaction products were separated by size exclusion chromatography after proceeding for the given time. Low molecular weight oligosaccharides are generated early on in the reaction (FIG. 7A). Both an increase in CPM for the oligosaccharide elution volume, and corresponding decrease in CPM for the higher molecular weight polymer over time suggest an exolytic type cleavage (FIG. 7A) that preferentially generates tetrasaccharides and hexasaccharides (FIG. 5A). A gradual shift of the peak from left to right over time would be indicative of true random endolytic cleavage.

Two-hour reactions were performed in three different buffers at pH 6.0, 7.2, and 8.0, detecting the concentration of reducing end glucuronic acid by the p-hydroxybenzoic acid hydrazide (PAHBAH) method (43) to determine the optimum reaction conditions for Pn3Pase. Pn3Pase displays slightly better activity in sodium phosphate buffer at pH 7.2 than in MES buffer pH 6.0, but performs significantly worse in Tris buffer at pH 8.0 in Tris buffer pH 8.0 (FIG. 7B). Further optimization focusing on metal-ion dependence was performed with Mg²⁺ and Ca²⁺. Pn3Pase displays a concentration-dependent preference for Ca²⁺, as it produces a higher concentration of reducing end GlcA in presence of 10 mM Ca²⁺ (FIG. 7C).

Pn3Pase Removes Capsule from Growing Type 3 Streptococcus pneumoniae

The type 3 WU2 strain was cultured for 10 h with 100 μg/ml of the recombinant enzyme added to the growth medium to begin assessing effects of Pn3Pase treatment of growing type 3 S. pneumoniae. Pn3Pase treatment of cells demonstrated no adverse growth or cytotoxic effects on the bacterial growth as indicated in FIG. 8A. Additionally, comparable CFU values were obtained at two-hour intervals (data not shown).

The bacterial cells grown in the presence of 2 μg/ml or 10 μg/ml Pn3Pase were then examined by competition ELISA to determine if the enzyme led to efficient capsule shedding of the growing cultures. After treatment, fixed whole cells, at different concentrations, were used to compete for Pn3P specific antibodies binding to the Pn3P coated plate. The acapsular WU2 mutant strain (JD908) showed minimal inhibition at 5×10⁵ CFU/ml and no inhibition at 5×10⁴ CFU/mL concentration, due to its lack of capsule (FIG. 8B). Heat inactivated Pn3Pase treated cells demonstrated the highest inhibition percent as cell surfaces should be fully decorated with CPS (FIG. 8B) With active Pn3Pase treatment, inhibition of antibody binding begins to decrease in a Pn3Pase concentration dependent manner (FIG. 8B), suggesting that the enzyme is well-designed to strip the capsule from live, growing type 3 Streptococcus pneumoniae.

A time course experiment was performed in which the bacterial cells were grown to mid-log phase, suspended in PBS, and treated with 1 μg/ml Pn3Pase for 0, 1, 2, or 4 hours. The Pn3Pase dose was lowered for this experiment given that the WU2 strain should not be actively growing and producing a substantial amount of new CPS under these conditions. The enzymatic activity of the Pn3Pase is also slightly better in PBS than in the THY culture media (data not shown). At the given time point, the treated cells were fixed and examined by competition ELISA as described above. The acapsular WU2 mutant strain (JD908), again, showed minimal inhibition at 5×10⁵ CFU/ml and no inhibition at 5×10⁴ CFU/mL concentration, due to its lack of capsule (FIG. 8C). Untreated cells exhibited the highest inhibition percent, indicative of a cell surface fully decorated with CPS (FIG. 8C) With increasing Pn3Pase incubation time, inhibition of antibody binding begins to decrease significantly (FIG. 8C), appearing essentially acapsular after 2 and 4 hour treatment.

The Pn3Pase treated cells were visualized by transmission electron microscopy and compared to both untreated and an acapsular mutant strain. The untreated cells displayed a thick, complete CPS coat across their surface (FIG. 8D upper left). As expected, the acapsular mutant had no CPS (FIG. 8D upper right). The capsule layer of the enzyme treated cells exhibited minimal thickness in most cases (FIG. 8D bottom left), while some looked as though they were acapsular (FIG. 8D bottom right).

Discussion

The Paenibacillus genus, literal Latin translation, “almost Bacillus,” was ruled distinct from true Bacillus species when phylogenetic analysis on 16S rRNA gene sequences was performed for a number of strains previously defined as Bacillus (6). Sequence analysis showed that several bacterial strains sorted into this genus, required reassignment. Species belonging to this genus have been obtained from diverse ecological niches (28) from aquatic (29) to desert environments (30), and from hot springs (31) to extreme cold regions (32). Many Paenibacillus species are found in soil (3,33) and plant root environments (34), however, a number are isolated from human samples as well (35). Paenibacillus species are a rich source for a variety of agricultural, biomedical, and industrial products (28). Extracellular enzymes demonstrating numerous activities (36) have applications in production of a variety of industrially significant materials (28). A number of these species are efficient nitrogen fixers that have been applied agriculturally to promote crop growth (37). In addition, protective action of novel antimicrobial peptides and compounds obtained from Paenibacilli has been demonstrated (38).

While Paenibacillus sp. 32352 was isolated from a soil source (3), it is appropriate to question the evolutionary pressure to obtain enzymes capable of acting on a human pathogen Spn CPS. Based on earlier studies, this particular strain demonstrates the ability to degrade three distinct pneumococcal CPSs (3,9). Whether these are the natural substrates for the enzymes, or whether other soil dwelling microbes or plant matter possess similar glycan residues and linkages remains to be investigated.

However originally acquired, Paenibacillus sp. 32352 has adapted the Pn3Pase described here to play an important functional role in its metabolism. Early reports by Torriani and Pappenheimer on this species indicated the ability to induce Pn3Pase activity in culture supernatant by addition of Pn3P in the growth medium (7). The “inducibility” was in contrast to the Avery and Dubose findings that Pn3Pase formation only occurred in conditions where Pn3P is present as a sole carbon source (2). Here, we demonstrate that while Pn3P is not required for bacterial growth, it can serve as the sole nutrition source. Moreover, our data indicate that presence of Pn3P in the Pbac culture medium induces the expression of Pn3Pase.

Our attempts to purify multi-milligram quantities of active, native Pn3Pase from an induced culture of this strain were unsuccessful, though Pn3P depolymerizing activity can be detected in these culture supernatant preparations. In this study, we have identified and cloned the Pn3Pase gene from Paenibacillus sp. 32352. We have fully characterized the oligosaccharide products, and we have shown that Pn3Pase can rapidly strip the CPS from live, growing Spn. Future studies will assess this enzyme's utility as a treatment for serotype 3 Spn infections. Inefficiencies in current vaccination and antibiotic administration necessitate the discovery of alternative therapeutic approaches for controlling these and other encapsulated pathogens.

Experimental Procedures Bacterial Strains and Growth Conditions

Paenibacillus sp. 32352 (ATCC 14175) was cultured aerobically with shaking at 37° C. on Tryptic Soy Agar with 5% sheep blood (Hardy Diagnostics), or in minimal medium (M9 Teknoba) culture containing 1 mM MgSO₄, 1 mM biotin, 1 mM thiamin, and 2% glucose (Sigma Aldrich) or Pn3P powder (ATCC 172-X) as sole carbon source. Streptococcus pneumoniae type 3 (WU2 strain) and acapsular derivative (JD908), generous gifts from Moon Nahm (University of Alabama at Birmingham), were cultured aerobically without shaking at 37° C. on Tryptic Soy Agar with 5% sheep blood (TSAB), or in Todd Hewitt Broth plus 0.5% yeast extract (THY) (BD Biosciences).

Proteomics of Culture Supernatants

Paenibacillus sp. 32352 was cultured in 5 ml of minimal medium M9 containing 2% (w/v) carbon source, as described above. Bacterial cultures were harvested at mid-log phase (OD600 nm 0.6). Culture supernatants were passed through a 0.45 μm syringe filter and concentrated to 1/20^(th) culture volume using a microsep advance centrifugal device with 10K molecular weight cutoff (Pall). Protein concentration was determined by bicinchoninic acid assay. An in-solution trypsin digestion was performed as described previously (39). Briefly, 20 μg protein from culture supernatant protein was reduced by incubation with 10 mM DTT for 1 h at 56° C., followed by carboxyamidomethylation with 55 mM iodoacetamide in the dark at room temperature for 45 min, and then digested with 1 □g of sequencing grade trypsin (Promega) in 40 mM ammonium bicarbonate overnight at 37° C. trypsin digest was stopped by addition of 1% trifluoroacetic acid and incubation on ice for 30 minutes. The resulting peptides were cleaned up using C18 spin columns (G Biosciences), dried down, and reconstituted in 0.1% formic acid. The peptides were separated using a Thermo Scientific UltiMate 3000 system on a 15 cm Acclaim™ PepMap™ RSLC C18 Column (2 μm particle size, 75 μm ID) using a 180 min linear gradient consisting of 1-100% Solvent B (80% acetonitrile, 0.1% formic acid) over 130 min at a flow rate of 200 nL/min. Separated peptides were directly eluted into a nanospray ion source of an Orbitrap Fusion Tribrid mass spectrometer (Thermo Fisher Scientific). The stainless steel emitter spray voltage was set to 2200 V, and the temperature of the ion transfer tube was set to 280° C. Full MS scans were acquired using Orbitrap detection from m/z 200 to 2000 at 60,000 resolution, and MS² scans following fragmentation by collision-induced dissociation (38% collision energy) were acquired in the ion trap for the most intense ions in “Top Speed” mode using Thermo Xcalibur Instrument Setup 3.0. The raw spectra were searched against the Rapid Annotation Server (40) (RAST) annotated genome database for Paenibacillus sp. 32352 using SEQUEST in Proteome Discoverer 1.4 (Thermo Fisher Scientific) with full MS peptide tolerance of 10 ppm and MS2 peptide tolerance of 0.3 Da. Constant modification of +57.021 Da (carbamidomethylation of cysteine residues), and dynamic modification of +15.995 Da (oxidation of methionine residues) were allowed in the search parameters. Results were filtered at a 1% false discovery rate for peptide assignments.

Gene Expression

Comparison of the levels of transcript expression from the Pn3P induced locus was performed by RT-PCR. Paenibacillus sp. 32352 was cultured in 5 ml of minimal medium containing 2% (w/v) carbon source, as described above. Triplicate bacterial cultures were harvested at mid-log phase (OD 600 nm 0.6), RNA was purified using E.N.Z.A. Bacterial RNA Kit, followed by TRIzol (Thermo Fisher Scientific) extraction of RNA from contaminating genomic DNA as described previously (41). RNA purity was assessed with nanodrop, and 1 μg of RNA was used for reverse transcription reaction using iscript CDNA synthesis kit (BioRad). Quantitative real time-PCR was performed in a 96-well plate on a MyiQ system (BioRad) with iQ SYBR green mastermix. Primers used in RT-PCR are listed in Table 3. The reactions were carried out in 20 μl, consisting of 10 μl of SYBR Green mix, 20 ng of cDNA, and 1 μM primer mix. The reaction conditions were 95° C. 180 s, followed by 45 cycles of 95° C. for 10 s, 55° C. for 20 s, and 72° C. for 30 s. The data were normalized to 16S rRNA transcript levels, and changes in expression level were calculated as fold change compared with cultures of minimal medium with glucose supplement.

TABLE 3 Oligonucleotides used. Oligonucleotide Sequence (5′ to 3′) Pbac_3551F-RT gcacccgtgaatctggaagc (SEQ ID NO: 10) Pbac_3551R-RT ctccataggaataagcgagagatagg (SEQ ID NO: 11) Pbac_3552F-RT gagccgtcaggcaccatac (SEQ ID NO: 12) Pbac_3552R-RT ctctaatgcaggctgcgg (SEQ ID NO: 13) Pbac_3554F-RT ggctgcggcggcacta (SEQ ID NO: 14) Pbac_3554R-RT tcccaaaacatcccggatcg (SEQ ID NO: 15) Pbac_1521F-RT gatggcgtgaaagacgatac (SEQ ID NO: 16) Pbac_1521R-RT acagttttgtcgttaacgcc (SEQ ID NO: 17) Pbac_16sF-RT catgagggaatcatgaaacacg (SEQ ID NO: 18) Pbac_16sR-RT gggctttcttctcaggtacc (SEQ ID NO: 19) Pbac_3551F ggggacaagtttgtacaaaaaagcaggcttcgaag gagatagaaccatggcacccgtgaatctggaagc (SEQ ID NO: 20) Pbac_3551R ggggaccactttgtacaagaaagctgggtgctcca cgatcaccttattcgataacg (SEQ ID NO: 21) Pbac_3552F ggggacaagtttgtacaaaaaagcaggcttcgaag gagatagaaccatggagccgtcaggcaccatac (SEQ ID NO: 22) Pbac_3552R ggggaccactttgtacaagaaagctgggtgcatcc ctcctgcgatgtg (SEQ ID NO: 23) Pbac_3554F ggggacaagtttgtacaaaaaagcaggcttcgaag gagatagaaccatgggctgcggcggcacta (SEQ ID NO: 24) Pbac_3554R ggggaccactttgtacaagaaagctgggtgcttct ttgcgctcttgttatactc (SEQ ID NO: 25)

Production of Recombinant Pn3Pase

The coding region of Pbac_3551 (ref seq WP_079915027), Pbac_3552 (ref seq WP_079915028), and Pbac_3554 (ref seq WP_079915030.1) (minus predicted signal peptide and stop codon) were amplified from Paenibacillus sp. 32352 genomic DNA (DNeasy blood and tissue kit, Qiagen) using 2× platinum superfi mastermix (Thermo Fisher Scientific) with overhang containing B-sites to facilitate gateway cloning (42) via BP reaction (Thermo Fisher Scientific) into pDONR221. Primers for cloning are listed in Table 3. After DH5a transformation and DNA sequence confirmation, an LR-clonase reaction was performed to insert the gene into the pET-DEST42 (Thermo Fisher Scientific) destination vector for the expression of a carboxy-terminal His6-tagged fusion protein in E. coli BL21(DE3) cells. BL21(DE3) cells transformed with the pET-DEST42-“Pn3Pase” plasmid were grown in LB medium supplemented with 100 μg/ml ampicillin at 37° C., and cell density was monitored by absorbance at 600 nm. Once the OD 600 nm reached 0.6, the cells were transferred into 25° C., protein expression was induced by the addition of Isopropyl β-D-1-thiogalactopyranoside to a final concentration of 1 mM and the cell culture was allowed to incubate for 8 h (until A600 reached ˜1.1). Cells were harvested by centrifugation. Cells were then resuspended in phosphate-buffered saline (PBS, pH 7.2) with 1 mg/ml lysozyme for 20 min at 30° C., probe sonicated for 2 min (four cycles of 20 s on, 10 s off), clarified by centrifugation at 17,000×g for 1 h at 4° C., and passed through a 0.45 μm syringe filter. Recombinant Pn3Pase was purified by Ni²⁺-NTA resin at 4° C., eluted with 300 mM imidazole and buffer exchanged into PBS pH 7.2. Protein concentration was determined by bicinchoninic acid assay. Purity was assessed by visualizing proteins on stain free tris-glycine gel (BioRad) using gel doc EZ imager (BioRad).

Enzyme Assays

Tritiated Pn3P assays—Recombinant enzyme activity against type 3 capsular polysaccharide was assayed by incubation of 2 μg/ml recombinant protein, or heat killed control, with 10 μg/ml ³H-Pn3P in PBS. The reaction was stopped after 2 h by heating at 100° C. for 5 minutes. Reaction mixture was separated on a superdex peptide 10/300 GL column (GE) on an NGC discoverer FPLC system (BioRad). Fractions of 1 ml were collected, and counts per minute in each fraction were counted in a Tri-Carb 2910 TR liquid scintillation analyzer (Perkin Elmer). Time course experiments were analyzed by the same method.

Reducing end sugar assays—recombinant Pn3Pase hydrolysis activity was determined by measuring the increase in reducing ends using the p-hydroxybenzoic acid hydrazide (PAHBAH) method (43). A reaction mixture (200 μl) containing 20 μg Pn3P, and 1 μg recombinant Pn3Pase in either 50 mM MOPS-NaOH (pH 6.0), 50 mM sodium phosphate buffer (pH 7.2), or 20 mM Tris-HCl (pH 8.0), was incubated at 37° C. for 1 h and then heated at 100° C. for 5 min to stop. Reaction mixture (40 μl) was mixed with 120 μl of 1% (w/v) PAHBAH-HCL solution, heated at 100° C. for 5 min. Absorbance at 405 nm was measured on a Biotek synergy H1 microplate reader in a clear bottom 96-well microplate. Concentrations of reducing sugars were calculated based on GlcA standard curves generated by the same method in respective buffers. Metal dependence assays were performed similarly with addition of MgCl₂ or CaCl₂ in phosphate buffer (pH 7.2).

Oligosaccharide Analysis

Pn3P powder (2 mg) was incubated with 100 μg of Pn3Pase at 37° C. for 48 h. The reaction was stopped by heating at 100° C. for 5 min, and loaded onto Superdex peptide 10/300 GL column (GE). Products were separated in phosphate buffered saline at a flow rate of 1 ml/min and monitored by refractive index. Fractions (0.5 ml) were collected and oligosaccharide peaks were purified, desalted into water on a packed fine P2 column (Biorad). Desalted oligos were lyophilized and subject to ESI-MS for mass determination and NMR for structural and reducing end identification.

NMR—Oligosaccharides were dissolved in 400 μL ²H₂O (99.9%, Sigma-Aldrich, St. Louis, Mo.) and lyophilized three-times to remove the exchangeable protons. The samples were re-dissolved in 400 μl 99.96% ²H₂O and transferred to NMR microtubes. ¹H spectroscopy, ¹³C spectroscopy, ¹H-¹H correlated spectroscopy (COSY), and ¹H-¹³C heteronuclear single quantum coherence spectroscopy (HSQC) experiments were all performed at 298 K on Bruker 600 or 800 MHz spectrometer with Topspin 2.1.6 software.

Pn3Pase Treatment of Type 3 S. pneumoniae

Fresh Streptococcus pneumoniae type 3 (WU2) and acapsular derivative (JD908) colonies on TSAB plates were inoculated to 0.1 OD in THY broth and cultured as described above. WU2 growth in presence of 100 μg/ml Pn3Pase was monitored over the course of 10 h by measuring OD 600 nm. WU2 grown in presence of 2 μg/ml, 10 μg/ml, or 10 μ/ml heat inactivated Pn3Pase, along with acapsular were grown for 6 hours, serially diluted, and plated to determine colony forming units. Cultures were harvested by centrifugation, washed in PBS, fixed in 2% paraformaldehyde for 20 min on ice, washed once more, and suspended in 1 ml PBS. For time course experiment, WU2 and acapsular strain were grown to mid-log phase (OD 600 nm of 0.6), harvested by centrifugation, washed in PBS, and then suspended in 1 ml PBS. 1 μg/ml Pn3Pase was added and incubated at 37° C. for the 1, 2, or 4 hours. Treated cells were serially diluted, and plated to determine colony forming units, fixed in 2% paraformaldehyde for 20 min on ice, washed once more, and suspended in 1 ml PBS.

Competition ELISA

ELISA plates (96 well, Nunc) were coated with 5 μg/ml Pn3P in 0.1 M carbonate buffer (pH 9.0) overnight at room temperature. Plates were washed 4-times with PBS+0.1% Tween (PBS-T) 20 using a Biotek 405/LS microplate washer. After 1 h blocking at room temperature with 1% BSA in PBS, microplate wells were incubated for 2 h at room temperature with fixed, treated cells that were pre-incubated for 30 min with Pn3P specific anti-serum in PBS-T. Plates were washed, and then incubated for 2 h at room temperature with 1:2000 dilution of goat anti-mouse IgG-AP (Southern Biotech #1030-04) in PBS-T. After washing, plates were incubated for ˜30 min at 37° C. with 2 mg/ml phosphatase substrate (Sigma S0942) in 1 M Tris 0.3 mM MgCl₂. Absorbance at 405 nm was measured on a Biotek synergy H1 microplate reader. Percent inhibition of antibody binding was calculated by ((Uninhibited_(OD405)−Inhibited_(OD405))/Uninhibited_(OD405))×100.

Electron Microscopy

Electron microscopy was performed by Georgia Electron Microscopy core facility at the University of Georgia according to a modified method by Hammerschmidt et al. (44). Treated cells were fixed in 2% glutaraldehyde and 0.15% ruthenium red in PBS buffer for 1 h on ice and then rinsed 2× with buffer containing 0.15% ruthenium red, 15 min per rinse. Cells were then fixed in 1% osmium tetroxide in buffer containing 0.15% ruthenium red for 1 h at room temperature followed by two rinses in buffer containing 0.15% ruthenium red, 15 min per rinse. Pellet was dehydrated in a graded ethanol series (30%, 50%, 75%, 95%, 100% and 100%) and two changes in 100% acetone, 15 min each step. Pellet was then infiltrated with 25% Spurr's resin and 75% acetone-2 h followed by sequential infiltration with 50% Spurr's resin and 50% acetone, 75% Spurr's resin and 25% acetone, 100% Spurr's resin and then polymerized in a 70° C. oven for 24 h. Samples were sectioned at 60 nm with a Diatome diamond knife and pick up on slot grids. Grids were post-stained on drops of uranyl acetate and lead citrate, 5 min each and rinsed with H₂O 30 s between stains. Samples were scoped using a JEOL JEM 1011 TEM (JEOL USA, Peabody, Mass.) operated at 80 kV.

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Example 2 Enzymatic Hydrolysis of Pneumococcal Capsular Polysaccharide Renders the Bacterium Vulnerable to Host Defense Abstract

Despite a century of investigation, Streptococcus pneumoniae (Spn) remains a major human pathogen, causing a number of diseases such as pneumonia, meningitis, and otitis media. Like many encapsulated pathogens, the capsular polysaccharide (CPS) of Spn is a critical component for colonization and virulence in mammalian hosts. This study aimed to evaluate the protective role of a glycoside hydrolase, Pn3Pase, targeting the CPS of type 3 Spn, which is one of the most virulent serotypes. We have assessed the ability of Pn3Pase to degrade the capsule on a live type 3 strain. Through in vitro assays we observed that Pn3Pase treatment increases the bacterium's susceptibility to phagocytosis by macrophages and complement-mediated killing by neutrophils. We have demonstrated that in vivo Pn3Pase treatment reduces nasopharyngeal colonization, and protects mice from sepsis caused by type 3 Spn. Due to the increasing shifts in serotype distribution, rise in drug resistant strains, and poor immune responses to vaccine-included serotypes, it is necessary to investigate approaches to combat pneumococcal infections. This study evaluates the interaction of pneumococcal CPS with host at molecular, cellular and systemic levels and offers an alternative therapeutic approach for diseases caused by Spn through enzymatic hydrolysis of the CPS.

Introduction

Streptococcus pneumoniae (Spn), the causal agent of pneumonia, meningitis, and otitis media, remains a major threat to human health. This bacterium can stably colonize the human nasopharynx as a part of the normal commensal microflora (1-3). Colonization is the primary mode of transmission and a key step in the initiation of disease, despite asymptomatic carriage (4, 5). A critical component for survival within the host and full pathogenicity of most Spn strains is the capsular polysaccharide (CPS) (6, 7). The CPS is a large and distinct polysaccharide structure coating the entire surface of the bacterium. The capsule helps Spn evade the host immune system through resisting or inhibiting its phagocytosis by host macrophages while also limiting mucus-mediated clearance (8-11). Spn has over 90 unique capsular serotypes, each differing in monosaccharide composition and linkage, as well as other modifications such as acetylation (12). The requirement of the CPS in bacterial virulence, surface accessibility, and antigenicity, has made it a target in vaccination studies for over 100 years (12-16). Great strides have been made at increasing the immunogenicity and efficacy of pneumococcal vaccines that utilize the CPS by conjugation to a protein carrier (17, 18). Current pneumococcal vaccines aim to provide serotype-specific protection for some of the most relevant clinical serotypes (12, 13). The use of the 7 and 13-valent pneumococcal conjugate vaccines, PCV7 and PCV13 (Prevnar; Pfizer) has been a major success; reducing invasive pneumococcal disease (IPD) rates significantly in both vaccinated and unvaccinated populations (15, 19-22).

While the conjugate vaccines have been effective for preventing carriage and IPD caused by most included serotypes, the exception has been serotype 3. The pneumococcal type 3 polysaccharide (Pn3P) component of the current PCV13 induces variable immune responses to Spn serotype 3, (23-25). Pn3P is a linear polymer of −3βGlcA(1-4)βGlc(1−disaccharide repeating units with an average molecular weight of >400 kDa (26, 27). It was noted that significantly higher serum titers are required for serotype 3 in comparison with other serotypes for opsonophagocytic killing of Spn (12, 28, 29). Numerous animal model and epidemiology studies have associated type 3 strains with increased virulence and death risk compared to other pneumococcal serotypes (30-32). A recent case report demonstrated a fatal case of IPD caused by serotype 3, highlighting increased complications and generally poor outcomes associated with this invasive serotype (33). In addition, recent data indicate that Spn strains are resistant to one or more antibiotics in 30% of IPD cases (34). The Centers for Disease Control and Prevention predict a rise in antibiotic-resistance features of Spn (35, 36).

The inability of vaccination to provide adequate protection against one of the most aggressive serotypes of this major human pathogen necessitates the urgent exploration of alternative approaches for type 3 pneumococcal infections. This, along with a rise in the prevalence of antibiotic resistant strains (37, 38) led us to revisit early studies by Avery and Dubos, who discovered a soil dwelling bacterium producing an enzyme that hydrolyzes Pn3P (39-41). Previously, we have identified this bacterium as a Paenibacillus species, cloned its type 3 specific glycosyl hydrolase, Pn3Pase, and characterized its degradation products (26, 42). In light of the continued prevalence, and severity of serotype 3 Spn, we postulated the potential use of this purified protein as a therapeutic agent for hyper virulent serotype 3 infections. Here, we investigated the ability of Pn3Pase to degrade the capsule on a live virulent type 3 Spn strain and therefore render the bacterium susceptible to host immune clearance.

Materials and Methods Bacterial Strains and Growth Conditions

Streptococcus pneumoniae type 3 (WU2 strain) and acapsular derivative (JD908) (60, 61), generous gifts from Moon Nahm (University of Alabama at Birmingham), were cultured aerobically without shaking at 37° C. on Tryptic Soy Agar with 5% sheep blood (TSAB), or in Todd Hewitt Broth plus 0.5% yeast extract (THY) (BD Biosciences).

Mice

Eight-week-old female BALB/c mice were obtained from Taconic Biosciences (Hudson, N.Y.) and housed in the Central Animal Facility at the University of Georgia. Mice were kept in microisolator cages and handled under BSL-2 hoods.

Production of Recombinant Pn3Pase

Pn3Pase was produced as described previously with minor modifications (26). Briefly, BL21(DE3) cells transformed with the pET-DEST42-“Pn3Pase” plasmid were grown in Terrific Broth supplemented with 100 μg/ml ampicillin at 37° C., and cell density was monitored by absorbance at 600 nm. Once the OD 600 nm reached 1.0, the cells were transferred into 18° C. Protein expression was induced by the addition of Isopropyl β-D-1-thiogalactopyranoside to a final concentration of 1 mM and the cell culture was allowed to incubate for 18 h. Cells were harvested by centrifugation, resuspended in phosphate-buffered saline (PBS, pH 7.2) and lysed by pressure lysis. The lysate was clarified by centrifugation at 17,000×g for 1 h at 4° C., and passed through a 0.45 μm syringe filter. Recombinant Pn3Pase was purified by Ni2+-NTA resin at 4° C., eluted with 300 mM imidazole and buffer exchanged into PBS pH 7.2. Protein concentration was determined by the bicinchoninic acid assay according to the instructions of the manufacturer. Purity was evaluated by coomassie staining.

Pn3Pase Treatment of Type 3 S. pneumoniae

Fresh Streptococcus pneumoniae type 3 (WU2) and acapsular derivative (JD908) colonies on TSAB plates were inoculated to 0.1 OD 600 nm in THY broth and cultured as described above. WU2 growth in presence of 100 μg/ml Pn3Pase was monitored over the course of 10 h by measuring OD 600 nm. WU2 was grown in presence of 2 μg/ml, 10 μg/ml, or 10 μg/ml heat inactivated Pn3Pase for 6 hours, serially diluted, and plated to determine colony forming units. Cultures were harvested by centrifugation, washed in PBS, fixed in 2% paraformaldehyde for 20 min on ice, washed once more, and suspended in 1 ml PBS. For the time course experiment, WU2 and the acapsular strain were grown to mid-log phase (OD 600 nm of 0.6), harvested by centrifugation, washed in PBS, and then suspended in 1 ml PBS. Then, 1 μg/ml Pn3Pase was added and incubated at 37° C. for the 1, 2, or 4 hours. Treated cells were serially diluted, and plated to determine colony forming units, fixed in 2% paraformaldehyde for 20 min on ice, washed once more, and suspended in 1 ml PBS.

Competition ELISA

ELISA plates (96 well, Nunc) were coated with 5 μg/ml Pn3P in 0.1 M carbonate buffer (pH 9.0) overnight at room temperature. Plates were washed 4-times with PBS+0.1% Tween (PBS-T) 20 using a Biotek 405/LS microplate washer. After 1 h blocking at room temperature with 1% BSA in PBS, microplate wells were incubated for 2 h at room temperature with fixed, treated cells that were pre-incubated for 30 min with Pn3P specific anti-serum in PBS-T. Plates were washed, and then incubated for 2 h at room temperature with 1:2000 dilution of goat anti-mouse IgG-AP (Southern Biotech #1030-04) in PBS-T. After washing, plates were incubated for ˜30 min at 37° C. with 2 mg/ml phosphatase substrate (Sigma S0942) in 1 M Tris 0.3 mM MgCl2. Absorbance at 405 nm was measured on a Biotek synergy H1 microplate reader. Percent inhibition of antibody binding was calculated by ((Uninhibited_(OD405)−Inhibited_(OD405))/Uninhibited_(OD405))×100.

Electron Microscopy

Electron microscopy was performed by the Georgia Electron Microscopy core facility at the University of Georgia according to a modified method by Hammerschmidt et al. (62). Treated cells were fixed in 2% glutaraldehyde, 2% paraformaldehyde, 0.075M lysine-acetate and 0.075% ruthenium red in PBS buffer for 1 h on ice and then rinsed 2× with buffer containing 0.15% ruthenium red, 15 min per rinse. Cells were then fixed in 1% osmium tetroxide in buffer containing 0.15% ruthenium red for 1 h at room temperature followed by two rinses in buffer containing 0.15% ruthenium red, 15 min per rinse. Pellet was dehydrated in a graded ethanol series (30%, 50%, 75%, 95%, 100% and 100%) and two changes in 100% acetone, 15 min each step. Pellet was then infiltrated with 25% Spurr's resin and 75% acetone-2 h followed by sequential infiltration with 50% Spurr's resin and 50% acetone, 75% Spurr's resin and 25% acetone, 100% Spurr's resin and then polymerized in a 70 □C oven for 24 h. Samples were sectioned at 60 nm with a Diatome diamond knife and picked up on slot grids. Grids were post-stained on drops of uranyl acetate and lead citrate, 5 min each and rinsed with H₂O 30 s between stains. Samples were scoped using a JEOL JEM 1011 TEM (JEOL USA, Peabody, Mass.) operated at 80 kV.

Phagocytosis

Mid-log phase WU2 and JD908 (acapsular) cultures were washed and stained with 10 Carboxyfluorescein succinimidlyl ester (CF SE) for 30 minutes at room temperature. The WU2 strain was concurrently treated with 2 μg/ml of active or heat-inactivated Pn3Pase. Bacterial cell pellets were washed extensively, suspended in 1 ml sterile PBS. 10⁷ bacteria were added to a confluent monolayer of murine leukemia virus transformed macrophage line, RAW 264.7 (American Type Culture Collection (ATCC) Manassas, Va.) with active or heat-inactivated baby rabbit complement (Pel-Freez) in a 24 well plate and incubated for 1 hour at 37° C. Wells were washed 4× with PBS to remove extracellular bacteria. Macrophages were fixed with 2% paraformaldehyde at 4° C. for 15 minutes and removed from the plate. For microscopy, cells were incubated at room temperature for 30 minutes with a 1/500 dilution of biotinylated wheat germ agglutinin (Vector labs) in 1% bovine serum albumin followed by a 30-minute room temperature incubation with a 1/1000 dilution of streptavidin APC (Biolegend). Cells were imaged with a 40× objective lens. Flow cytometry was performed on a Beckman Cytoflex S cytometer and analyzed by FlowJo. Cells were gated on the macrophage population by scatter plot. A non-CF SE labeled control served to gate highly fluorescent cell populations. The Pn3Pase dose dependent experiment was performed as above with addition of active complement.

Complement Deposition

A complement deposition assay was performed as described previously (63). Type 3 WU2 and acapsular (JD908) strains of bacteria were resuspended in 3% BSA in PBS. Aliquots (in duplicate wells on a 96-well round-bottom plate) were stained with Hoechst 33342 and treated with inactivated or functional Pn3Pase at 5 or 50 μg/ml for 1 hour at 37° C. Normal mouse serum (1:10 dilution) was added to the samples for 30 minutes at 37° C. Cells were washed and stained with FITC-conjugated goat antibody to mouse complement (MP BioMedical, Santa Ana, Calif.) at 4° C. for 30 minutes. Samples were washed with 3% BSA in PBS and resuspended in 2% paraformaldehyde to fix. Samples were then analyzed with flow cytometry. Mean fluorescent intensity (MFI) of FITC-A was calculated from gating of Hoechst-positive cells.

Modified OPA

An opsonophagocytic killing assay was performed as described previously with modifications (43). Briefly, the type 3 WU2 and acapsular (JD908) strains were incubated in duplicate wells in a 96-well round-bottom plate for 1 hour or 4 hours at 37° C. with or without Pn3Pase (inactivated or functional at concentrations of 5 or 50 ug/ml) in opsonization buffer B (OBB, sterile 1×PBS with Ca++/Mg++, 0.1% gelatin, and 5% heat-inactivated FetalClone). Human promyelocytic leukemia cell line, HL-60 (ATCC Manassas, Va.) were cultured in RPMI with 10% heat-inactivated FetalClone (HyClone) and 1% L-glutamine. HL-60 cells were differentiated using 0.6% N,N-dimethylformamide (DMF, Fisher) for three days before performing the OPA assay, harvested, and resuspended in OBB. Active or heat-inactivated (no complement) baby rabbit complement (Pel-Freez) was added to HL-60 cells at 1:5 final volume. The HL-60/complement mixture was added to the serum/bacteria at 5×10⁵ cells/well (for controls, no HL-60/complement was added; equal volumes of OBB buffer was added instead). The final reactions were incubated at 37° C. for 1 hour. The reactions were stopped by incubating the samples on ice for approximately 20 minutes. Then, 10 μl of each reaction was diluted to a final volume of 50 μl and plated onto blood agar plates in duplicate. Plates were incubated overnight at 30° C. in anaerobic conditions and counted the next day. Percent survival was calculated as each duplicate reaction normalized to mean values obtained for control samples (reactions without HL-60 cells, 100% survival).

Murine Intranasal Colonization

An intranasal colonization was performed essentially as described by Puchta et al (64). Mid-log phase WU2 cultures were washed with sterile PBS and suspended at a concentration of 10⁸ CFU/ml or 10⁶ CFU/10 μl. Groups of 5 to 10 unanesthetized 8-week-old female BALB/c mice (Taconic) were intranasally inoculated with 10⁶ CFU/10 μl as previously described. Mice were either inoculated with 10 μl of PBS as vehicle on day 0, 3, and 7 or treated by administering 50 μg of Pn3Pase in 10 μl PBS on day 0, 0 and 3, or 0, 3, and 7. Nasal lavage fluid was obtained on day 10 by flushing out the nasopharynx with PBS by insertion of a 25 gauge needle into the trachea to expel 500 μl through the nares. Serial dilutions of the nasal lavage fluid were plated on Tryptic Soy Agar with 5% sheep blood (TSAB), to enumerate the colony forming units. A sandwich ELISA (Biolegend mouse ELISA MAX) was performed according to manufacturer's instructions to determine IL-6 and TNFα cytokine levels in the lavage fluid.

Murine Sepsis Challenge

Mid-log phase WU2 cultures were washed with sterile PBS and suspended at a concentration of 5×10³ CFU/100 μL. Groups of 4 unanesthetized 8-week-old female BALB/c mice (Taconic) were injected intraperitoneally (I.P.) with 5×10³ CFU. Control mice were injected I.P. with 5 μg of heat inactivated Pn3Pase in 100 μL of PBS at time 0, or directly after infection. Treated mice were administered I.P. 0.5 μg or 5 μg of Pn3Pase in 100 μL PBS at time 0, 12, or 24 hours post infection. Animals were monitored every 12 hours.

Results

Pn3Pase Removes Capsule from Growing Type 3 Spn

The encapsulated type 3 WU2 strain was cultured for 10 hours with the recombinant enzyme added to the growth medium and bacterial growth was monitored by measuring OD at 600 nm to assess effects of Pn3Pase treatment on growing type 3 Spn. Pn3Pase treatment of cells demonstrated no adverse growth or cytotoxic effects on the bacteria (FIG. 9A). In the same experiment, we obtained comparable CFU values for both enzyme treated and non-treated groups at two-hour intervals (data not shown). To assess direct impact of enzyme treatment on bacterial survival, a log-phase culture was isolated and suspended in nutrient-free buffer with active, or heat inactivated Pn3Pase. Enzyme treated cells showed comparable counts to inactivated and PBS controls over the 8-hour time course (FIG. 9B).

The bacterial cells grown in the presence of Pn3Pase were then examined by competition ELISA to determine if the enzyme led to efficient capsule removal in the growing cultures. After treatment, fixed whole cells, at two different concentrations, were used to compete for Pn3P specific antibodies binding to the Pn3P coated plate. The acapsular WU2 mutant strain (JD908) showed minimal to no inhibition of antibody binding due to its lack of capsule. Heat inactivated Pn3Pase treated cells demonstrated the highest percent inhibition as cell surfaces should be fully decorated with CPS. With active Pn3Pase treatment, inhibition of antibody binding begins to decrease in a Pn3Pase concentration dependent manner (FIG. 10A), suggesting that the enzyme strips the capsule from live, growing type 3 Spn.

A time course experiment was performed in which the bacterial cells were grown to mid-log phase, suspended in PBS, and treated with Pn3Pase for 0, 1, 2, or 4 hours. The Pn3Pase dose was lowered to 1 μg/ml for this assay given that the WU2 strain should not be actively growing and therefore not producing a substantial amount of new CPS under these conditions. At each time point, the treated cells were fixed and examined by competition ELISA as described above. The acapsular WU2 mutant strain (JD908), again, showed minimal to no inhibition due to its lack of capsule. Untreated cells exhibited the highest percent inhibition, indicative of a cell surface fully decorated with CPS. With increasing Pn3Pase incubation time, inhibition of antibody binding begins to decrease significantly, appearing essentially acapsular after 2- or 4-hour treatments (FIG. 10B).

The Pn3Pase treated cells were visualized by transmission electron microscopy and compared to the cells treated with heat inactivated Pn3Pase. The heat inactivated enzyme treated cells displayed a thick, complete CPS coat across their surface (FIG. 10C), undoubtedly distinct from the acapsular mutant (FIG. 10D). The capsule layer of the enzyme treated cells exhibited little to no capsule (FIG. 10E), appearing as acapsular.

Pn3Pase Treatment of Type 3 Spn Allows Phagocytic Cell Uptake and Killing

A major virulence mechanism of the CPS is to provide the bacterium the ability to resist phagocytosis by host phagocytic cells (1, 6). To investigate the effect of Pn3Pase treatment on uptake by macrophages in vitro, we stained mid-log phase bacterial cultures with carboxyfluorescein succinimidlyl ester (CF SE) and then treated with Pn3Pase followed by incubation with RAW 264.7 macrophages. Macrophages were then washed extensively and imaged by fluorescent microscopy (FIG. 11A). The extent of bacterial uptake by macrophages was quantified by flow cytometry. Bacteria treated with the enzyme were taken up by macrophages significantly more than the encapsulated strain. We then determined the percentage of fluorescent macrophages, representing the phagocytosis of fluorescent bacteria (FIGS. 11C-D). The encapsulated type 3 strain incubated with heat inactivated Pn3Pase had minimal fluorescently labeled phagocytes whereas Pn3Pase treated bacteria were as efficiently taken up by the macrophages as the acapsular mutant strain. Uptake was partially dependent on complement as evidenced by higher bacterial uptake in the presence of complement (FIG. 11C). Pn3Pase treatment rendered the bacteria more susceptible to phagocytic engulfment by RAW macrophages in a dose dependent manner, while even high doses of the inactivated enzyme had no significant effect on bacterial uptake (FIG. 11D).

Complement deposition on the pneumococcal surface is an important mechanism aiding in efficient phagocytosis and clearance (10, 11). Since CPS provides complement evasive properties to the bacterium (10, 11), we investigated the effect of capsule removal by Pn3Pase treatment on C3b deposition on the bacterial surface. The encapsulated type 3 WU2 strain was treated with active or inactive Pn3Pase. The untreated type 3 strain and the acapsular mutant were included as additional controls. Bacteria were then incubated with normal mouse serum, washed, and stained with FITC-conjugated antibody to mouse complement. Fixed samples were then analyzed with flow cytometry. In a dose dependent manner, Pn3Pase treatment increased the deposition of complement on the bacterial surface, reaching the levels of deposition on the acapsular strain. Complement had minimal binding to the bacteria either untreated or treated with inactivated-Pn3Pase (FIG. 12).

The standard in vitro assay to assess phagocytic killing of Spn is an opsonophagocytosis assay (OPA) in which HL-60 cells are differentiated into neutrophils to engulf and clear antibody opsonized bacteria. This method has been widely used to measure the quality of antibody responses in numerous vaccine studies (43-48). Neutrophils are one of the most important components of innate immunity against pathogenic bacteria in the lungs (49-51). While the focus of this study is not on humoral immune responses to Spn, we have used a modified OPA to evaluate complement-mediated neutrophil killing of type 3 Spn treated with Pn3Pase in vitro. Encapsulated type 3 Spn was incubated with active or heat inactivated Pn3Pase. Differentiated HL-60 cells were pre-incubated with active or heat-inactivated complement. The mixture of HL-60 cells and complement was added to the bacteria and incubated at 37° C. for 1 hour. To quantify the surviving bacteria in the experimental groups, the reaction mixtures were plated and CFUs were counted the next day. Percent survival was calculated as each duplicate reaction normalized to mean values obtained from reactions without neutrophils, which served as control samples (100% survival). The enzyme-untreated, encapsulated type 3 strain was able to escape neutrophil killing to show maximum survival while the acapsular mutant strain was reduced to nearly 40% viability upon incubation with active complement and neutrophils (FIG. 13). Pn3Pase treatment to remove the capsule rendered the type 3 strain susceptible to complement dependent neutrophil killing similar to the acapsular strain (FIG. 13).

Pn3Pase Limits Nasopharyngeal Colonization

To investigate the enzyme's protective abilities in vivo we first performed an intranasal colonization experiment with BALB/c mice. Nasal colonization by Spn is essential for transition to invasive pneumococcal disease (4, 5). It is established that the capsule of this strain is required for intranasal colonization (6). Therefore, we used the nasal colonization model to assess the ability of Pn3Pase to reduce bacterial colonization in the nasopharynx through removal of the capsule of the colonizing type 3 strain. We first confirmed that the acapsular mutant, JD908, failed to colonize the nasopharynx (data not shown). Groups of mice were then intranasally inoculated with 10⁶ log-phase wildtype (wt) encapsulated bacteria in 10 μl PBS. All inocula were chased with either Pn3Pase or buffer control. Groups were dosed with the enzyme at either day 0, day 0 and 3, or day 0, 3, and 7 to assess the effects of multiple administrations. Mice were euthanized, and bacterial load was quantified on day 10. Nasal lavage fluid was obtained, serially diluted, and plated to enumerate the bacterial load. Vehicle control treated mice were colonized with significantly higher bacterial loads than mice treated with only a single dose of Pn3Pase. Administration of two or three doses of Pn3Pase made the majority of the animal lavage fluid void of any viable bacterial colonies (FIG. 14A). Lung homogenates and serum samples showed no evidence of a bacterial burden (data not shown). Signature pro-inflammatory cytokine levels were measured in the nasal lavage fluid by ELISA (52). Vehicle treated mice had significantly increased levels of the cytokines IL-6 and TNFα compared to Pn3Pase treated animals, a reflection of a continued host inflammatory response to the bacterial burden in this group (FIGS. 14B-C) (52). A significant reduction in IL-6 and TNFα was observed in most animals even after a single dose of Pn3Pase on day 0. The mouse with higher bacterial load in the single dose group contributed to the increased cytokine levels in this group.

Pn3Pase Protects Mice from Lethal Challenge

To further assess Pn3Pase for its protective abilities and evaluate the utility of Pn3Pase as a therapeutic agent, we employed an intraperitoneal (I.P.) sepsis model (53, 54). Groups of mice were infected with 5×10³ CFU of log-phase WU2 type 3 strain of Spn. We assessed the effect of a single dose of 5 μg or 0.5m, administered at time 0, 12, or 24 hours post infection. Control groups treated with heat inactivated enzyme died within 48 hours of infection. Regardless of the enzyme dose or the timing of the administration, all treated groups displayed no signs of illness and experienced full protection from the I.P. challenge (FIG. 15).

Discussion

This study aimed to evaluate the protective role of a carbohydrate-degrading enzyme (glycoside hydrolase), Pn3Pase, targeting the CPS of the pathogenic bacterium, serotype 3 Spn. Invasive pneumococcal diseases (IPD) caused by Spn have been a major threat to human health with alarming mortality rates. Despite a global vaccination program and the use of antibiotics, Spn remains among the deadliest infectious agents worldwide. Pneumococcal vaccines are made empirically and are variably/poorly immunogenic, especially among elderly and immunocompromised individuals. Widespread use of antibiotics against IPD has led to spread of drug resistant pneumococcal strains (34, 35). This study offers an alternative targeted therapeutic approach to the shortcomings of the incumbent vaccine and antibiotic solutions to IPD.

First we demonstrated that Pn3Pase could efficiently remove the capsule from live pneumococci without having bactericidal effects on the cells. Through in vitro assays we observed that Pn3Pase treatment increases the bacterium's susceptibility to phagocytosis by a macrophage cell line. These results were promising since the capsule is a major host immune evasion component that allows Spn to resist engulfment by host phagocytes (9). We then concluded that enzyme treatment significantly increased complement-mediated killing by the neutrophils. A single dose of Pn3Pase reduced murine nasopharyngeal colonization by type 3 Spn significantly, indicating that the enzyme may function as a prophylactic measure to control colonization by this serotype in at-risk populations. Finally, an intraperitoneal challenge was performed to assess the protective capacity of Pn3Pase in a sepsis model. Notably, a single low dose of 0.5 μg administered 24 hours after infection was able to protect 100% of the challenged mice from the bacterial challenge while control treated animals did not survive longer than 48 hours. The robust protective capacity of Pn3Pase in this model demonstrates the enzymatic activity is sufficient within the host to effectively degrade the capsule even at low doses.

Given that Pn3Pase has therapeutic potential for pneumococcal infections, practical issues pertaining to the application of the enzyme such as immunogenicity, administration routes, and substrate specificity will need to be addressed (55). Our preliminary assessment of antibody titers generated against Pn3Pase in the challenge experiments observed no IgM or IgG response generated against the effective dose of the enzyme. Future studies will evaluate humoral and cellular immune responses to Pn3Pase and investigate alternative routes of administration such as intravenous for a bacteremia model, or aerosolized spray for the pneumonia model. A useful example of enzyme delivery to the respiratory tract by aerosol spray is the recombinant human deoxyribonuclease known as Pulmozyme, used to relieve airway obstruction by secreted DNA in cystic fibrosis patients (56). Another potential problem with the use of Pn3Pase as a therapeutic agent is its activity on host glycans. Relaxed substrate specificity of Pn3Pase on mammalian glycans structurally similar to Pn3P will need to be assessed.

In addition to the high potential of Pn3Pase as a therapeutic enzyme, this glycosyl hydrolase has unique properties from a structure/function point of view in that it does not fall into a currently established glycosyl hydrolase Carbohydrate Active enZYme (CAZY) family (57). Further examination of structural properties of this protein may lead to the discovery of structurally similar enzymes with activities toward other unique bacterial CPSs. Future investigations will explore the existence of enzymes for use against other prevalent pneumococcal serotypes and other encapsulated pathogenic bacteria. Based on earlier studies, the native species expressing Pn3Pase has the capacity to degrade two additional pneumococcal CPSs (58, 59). While this Pn3Pase expressing Paenibacillus species was isolated from the soil (26, 42, 59), it is befitting to question why this species would evolve to possess such enzymes that are capable of degrading capsules of a human pathogen. Whether these are the natural substrates for the enzymes, indicating co-evolutionary relationship, or whether other soil-dwelling microbes or plants express similar glycan residues and linkages remains to be explored.

The results presented here indicate that enzymatic hydrolysis of the CPS may be a valid alternative or complementary therapeutic approach for diseases caused by Spn and potentially other important encapsulated pathogens such as Neisseria meningitidis and Methicillin-Resistant Staphylococcus aureus (MRSA). In summary, this study serves as the first comprehensive evaluation of the protective role of a glycoside hydrolase, Pn3Pase, debilitating an otherwise lethal bacterial pathogen through targeting its capsular polysaccharide.

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The complete disclosure of all patents, patent applications, and publications, and electronically available material (including, for instance, nucleotide sequence submissions in, e.g., GenBank and RefSeq, and amino acid sequence submissions in, e.g., SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq) cited herein are incorporated by reference in their entirety. Supplementary materials referenced in publications (such as supplementary tables, supplementary figures, supplementary materials and methods, and/or supplementary experimental data) are likewise incorporated by reference in their entirety. In the event that any inconsistency exists between the disclosure of the present application and the disclosure(s) of any document incorporated herein by reference, the disclosure of the present application shall govern. The foregoing detailed description and examples have been given for clarity of understanding only. No unnecessary limitations are to be understood therefrom. The disclosure is not limited to the exact details shown and described, for variations obvious to one skilled in the art will be included within the disclosure defined by the claims.

Unless otherwise indicated, all numbers expressing quantities of components, molecular weights, and so forth used in the specification and claims are to be understood as being modified in all instances by the term “about.” Accordingly, unless otherwise indicated to the contrary, the numerical parameters set forth in the specification and claims are approximations that may vary depending upon the desired properties sought to be obtained by the present disclosure. At the very least, and not as an attempt to limit the doctrine of equivalents to the scope of the claims, each numerical parameter should at least be construed in light of the number of reported significant digits and by applying ordinary rounding techniques.

Notwithstanding that the numerical ranges and parameters setting forth the broad scope of the disclosure are approximations, the numerical values set forth in the specific examples are reported as precisely as possible. All numerical values, however, inherently contain a range necessarily resulting from the standard deviation found in their respective testing measurements.

All headings are for the convenience of the reader and should not be used to limit the meaning of the text that follows the heading, unless so specified. 

1. (canceled)
 2. A genetically modified cell comprising a polynucleotide comprising a coding region, wherein the coding region comprises a nucleotide sequence encoding a mature Pn3Pase protein, and wherein the protein has Pn3Pase activity.
 3. The genetically modified cell of claim 2 wherein the protein comprises an amino acid sequence having at least 80% identity with an amino acid sequence selected from SEQ ID NO:2, wherein the amino terminal amino acid is selected from any one of residues 2 to 64 of SEQ ID NO:2 and the carboxy terminal amino acid is residue 1545 of SEQ ID NO:2.
 4. (canceled)
 5. The genetically modified cell of claim 2 wherein the cell is a eukaryotic cell.
 6. The genetically modified cell of claim 5 wherein the cell is a mammalian cell, a yeast cell, or an insect cell.
 7. The genetically modified cell of claim 2 wherein the cell is a prokaryotic cell.
 8. The genetically modified cell of claim 7 wherein the cell is E. coli.
 9. The genetically modified cell of claim 2 wherein the protein comprises a heterologous amino acid sequence.
 10. The genetically modified cell of claim 9 wherein the heterologous amino acid sequence comprises a tag. 11.-29. (canceled)
 30. A method comprising: contacting a Streptococcus pneumoniae comprising a type III capsular polysaccharide with a mature Pn3Pase protein comprising Pn3Pase activity, wherein the contacting is under conditions suitable for enzymatic hydrolysis of type III capsular polysaccharide, wherein the amount of type III capsular polysaccharide on the surface of the S. pneumoniae is reduced compared to the S. pneumoniae that is not contacted with the Pn3Pase protein.
 31. (canceled)
 32. The method of claim 30 wherein the protein comprises an amino acid sequence having at least 80% identity with an amino acid sequence selected from SEQ ID NO:2, wherein the amino terminal amino acid is selected from any one of residues 2 to 64 of SEQ ID NO:2 and the carboxy terminal amino acid is residue 1545 of SEQ ID NO:2.
 33. (canceled)
 34. The method of claim 30 wherein the S. pneumoniae is present in conditions suitable for replication of the S. pneumoniae.
 35. The method of claim 30 wherein the mature Pn3Pase protein is an isolated Pn3Pase protein.
 36. The method of claim 30 wherein the contacting comprises exposing the S. pneumoniae to a genetically modified cell that expresses the mature Pn3Pase protein.
 37. The method of claim 30 wherein the S. pneumoniae has increased susceptibility to phagocytosis by macrophages, increased complement-mediated killing by neutrophils, or a combination thereof, compared to the S. pneumoniae that is not contacted with the Pn3Pase protein.
 38. The method of claim 30 wherein the S. pneumoniae is present in a subject.
 39. A method for treating an infection or a symptom in a subject, the method comprising: administering an effective amount of a composition comprising a mature Pn3Pase protein having Pn3Pase activity to a subject having or at risk of having an infection caused by a serotype 3 S. pneumoniae. 40.-41. (canceled)
 42. The method of claim 39 wherein the protein comprises an amino acid sequence having at least 80% identity with an amino acid sequence selected from SEQ ID NO:2, wherein the amino terminal amino acid is selected from any one of residues 2 to 64 of SEQ ID NO:2 and the carboxy terminal amino acid is residue 1545 of SEQ ID NO:2.
 43. (canceled)
 44. The method of claim 39 wherein the subject is a human. 45.-50. (canceled)
 51. The method of claim 30 wherein the S. pneumoniae is in vitro.
 52. The method of claim 38 wherein the contacting comprises topical administration of a composition comprising the mature Pn3Pase. 